# Molecular Atlas A CONNECTED RESEARCH COLLECTION ## Explore the molecular atlas. Eight starting points. Explore their genes, protein structures, and source evidence. The collection groups research subjects. Spatial arrangement does not imply a physical interaction. ## REPRESENTATION Backbone and base rings from the atomic model. ## GENE REFERENCE Exons in gold · introns between · 5′ → 3′ The selected sequence, built as an ideal B-DNA atomic model. ## LAYERS ## GEOMETRY Choose a construction and enable the geometry layer. PHI RATIO φ = 1.618033… ## OXT · OXTR ### The molecular encounter Explore oxytocin at its receptor, from the complete complex to the aromatic contact. #### DOCKING SEQUENCE Bound pose · experimental coordinates Tilted Tyr2–Phe291 contact. Gold dashes measure a gap, not a chemical bond or an electron path. Pale green dashes mark the Tyr2–Leu316 hydrogen-bond contact. ## LEARN THE RING ### From atoms to orbitals The lobes and motion guides are schematic. Colour shows orbital sign, not electrical charge. Ring hydrogens are implicit. ## ELECTRONIC STRUCTURE ### Inside the aromatic system Explore calculated orbitals around a Tyr2–Phe291 fragment pair. Orbital amplitude · Bohr⁻³ᐟ² ### Oxytocin at OXTR Oxytocin is a cyclic peptide with the sequence CYIQNCPLG–NH₂ and a Cys1–Cys6 disulfide. Tyr2 sits deep in the receptor pocket. #### AROMATIC CONTACT Gold dashes are a distance guide between the closest ring carbons, not a chemical bond or an electron path. Pale green dashes identify the Tyr2–Leu316 hydrogen-bond contact. Distances use the deposited heavy atoms. Ring angles use least-squares planes through the six ring carbons. Structural resolution and model uncertainty limit their interpretation. #### ANIMATION The final bound pose uses 7QVM coordinates. The approach is a rigid, illustrative translation along an outward vector. It is not a molecular-dynamics trajectory, docking search, free-energy calculation or observed entry pathway. Only the bound pose displays contact measurements. 7QVM is an engineered human receptor complex determined by cryo-EM at 3.25 Å. G protein and antibody components are omitted from this view. [RCSB · 7QVM ↗](https://www.rcsb.org/structure/7QVM) The regular phenol ring and peptide attachment cue help explain the tyrosine side chain. They are idealised teaching geometry, with ring hydrogens implicit. #### SIX P ORBITALS Each aromatic carbon contributes a p orbital perpendicular to the ring plane. The two lobes have opposite wavefunction signs. Their colours do not represent positive and negative electrical charges. #### THE SHARED π SYSTEM #### MOTION GUIDES Moving markers guide the explanation. Their number, route and speed are symbolic, not electron counts, electron trajectories or physical timescales. No stimulus or time-dependent calculation is being simulated. #### CALCULATED VIEW The separate Calculated mode retains the PBE0/def2-SVP fields for the capped Tyr2–Phe291 fragment pair. The teaching geometry does not replace those data. ### A local quantum model #### CALCULATION #### ORBITALS [Source heavy-atom geometry · 7QVM ↗](https://www.rcsb.org/structure/7QVM) [PySCF · density functional theory ↗](https://pyscf.org/user/dft.html) ## Source data - [Reference genes](https://universalmind.tv/informatics/molecular/data/genes/index.json) ## Downloads [JSON](https://universalmind.tv/informatics/atlas-guides/molecular-atlas.json?v=2026-11-01-page-narrative-4) · [CSV](https://universalmind.tv/informatics/atlas-guides/molecular-atlas.csv?v=2026-11-01-page-narrative-4) · [MD](https://universalmind.tv/informatics/atlas-guides/molecular-atlas.md?v=2026-11-01-page-narrative-4) [Interactive page](https://universalmind.tv/informatics/molecular/) · [Wiki](https://universalmind.tv/informatics/read/molecular/index.html) ## Complete guide data ```json { "collection": { "version": 1, "title": "Molecular Atlas", "records": [ { "id": "OXTR", "pdb": "7QVM", "name": "Oxytocin receptor", "context": "Oxytocin signalling", "genes": [ "OXTR" ], "geneIds": [ 5021 ], "chains": [ "E" ], "ligandChains": [ "D" ], "contextChains": [ "A", "B", "C", "F" ], "note": "Engineered receptor complex. Receptor chain R and oxytocin chain L are shown initially. The complete deposited model also contains a G-protein chimera and an antibody fragment.", "title": "Human Oxytocin receptor (OTR) oxytocin Gq chimera (mGoqi) complex", "resolution": 3.25, "method": "ELECTRON MICROSCOPY", "source": "https://www.rcsb.org/structure/7QVM", "sha256": "9df96fcec74a5008a318b50311b95a9faa814126517460c9732414c3190f4242", "retrieved": "2026-10-21", "sequenceType": "Deposited protein construct", "sequences": [ { "chain": "E", "authorChain": "R", "name": "Oxytocin receptor", "sequence": "MEGALAANWSAEAANASAAPPGAEGNRTAGPPRRNEALARVEVAVLCLILLLALSGNACVLLALRTTRQKHSRLFFFMKHLSIADLVVAVFQVLPQLLWDITFRFYGPDLLCRLVKYLQVVGMFASTYLLLLMSLDRCLAICQPLRSLRRRTYRLAVLATWLGCLVASAPQVHIFSLREVADGVFDCWAVFIQPWGPKAYITWITLAVYIVPVIVLATCYGLISFKIWQNLRLKTAAAAAAEAPEGAAAGDGGRVALARVSSVKLISKAKIRTVKMTFIIVLAFIVCWTPFFFVQMWSVWDANAPKEASAFIIVMLLASLNSCCNPWIYMLFTGHLFHELVQRFLCCSASYLKGRRLGK", "length": 359 } ], "citation": { "country": "UK", "id": "primary", "journal_abbrev": "Nat Commun", "journal_id_ISSN": "2041-1723", "journal_volume": "13", "page_first": "4153", "page_last": "4153", "pdbx_database_id_DOI": "10.1038/s41467-022-31325-0", "pdbx_database_id_PubMed": 35851571, "rcsb_ORCID_identifiers": [ "0000-0001-5564-4303", "?", "0000-0002-6570-7336", "0000-0002-2221-6238", "0000-0003-0994-2937", "0000-0003-4191-5306" ], "rcsb_authors": [ "Waltenspuhl, Y.", "Ehrenmann, J.", "Vacca, S.", "Thom, C.", "Medalia, O.", "Pluckthun, A." ], "rcsb_journal_abbrev": "Nat Commun", "title": "Structural basis for the activation and ligand recognition of the human oxytocin receptor.", "year": 2022 }, "depositedLigands": [] }, { "id": "SLC6A4", "pdb": "5I6X", "name": "Serotonin transporter", "context": "Serotonin transport", "genes": [ "SLC6A4" ], "geneIds": [ 6532 ], "chains": [ "A" ], "ligands": [ "8PR" ], "contextChains": [ "B", "C" ], "note": "Thermostabilised human serotonin transporter with paroxetine. Antibody chains are available in the complex layer. This is an engineered experimental construct.", "title": "X-ray structure of the ts3 human serotonin transporter complexed with paroxetine at the central site", "resolution": 3.14, "method": "X-RAY DIFFRACTION", "source": "https://www.rcsb.org/structure/5I6X", "sha256": "29b8d278efa9ed9a9c5a64ea72718e84a6563dda26a7b978d71c7520cadecf61", "retrieved": "2026-10-21", "sequenceType": "Deposited protein construct", "sequences": [ { "chain": "A", "authorChain": "A", "name": "Sodium-dependent serotonin transporter", "sequence": "GSQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICAQNGGGAFLLPYTIMAIFGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIALSVLLVRGATLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLDSSFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIIASFLMSPPQLRLFQYNYPYWSIILGYAIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETPTLVPR", "length": 549 } ], "citation": { "country": "UK", "id": "primary", "journal_abbrev": "Nature", "journal_id_ASTM": "NATUAS", "journal_id_CSD": "0006", "journal_id_ISSN": "1476-4687", "journal_volume": "532", "page_first": "334", "page_last": "339", "pdbx_database_id_DOI": "10.1038/nature17629", "pdbx_database_id_PubMed": 27049939, "rcsb_ORCID_identifiers": [ "?", "?", "?" ], "rcsb_authors": [ "Coleman, J.A.", "Green, E.M.", "Gouaux, E." ], "rcsb_journal_abbrev": "Nature", "title": "X-ray structures and mechanism of the human serotonin transporter.", "year": 2016 }, "depositedLigands": [ { "id": "NAG", "name": "2-acetamido-2-deoxy-beta-D-glucopyranose" }, { "id": "CLR", "name": "CHOLESTEROL" }, { "id": "LMT", "name": "DODECYL-BETA-D-MALTOSIDE" }, { "id": "8PR", "name": "Paroxetine" }, { "id": "CL", "name": "CHLORIDE ION" }, { "id": "NA", "name": "SODIUM ION" } ] }, { "id": "DRD2", "pdb": "6CM4", "name": "Dopamine D2 receptor", "context": "Dopamine signalling", "genes": [ "DRD2" ], "geneIds": [ 1813 ], "chains": [ "A" ], "ligands": [ "8NU" ], "contextChains": [], "note": "Risperidone-bound D2 receptor–endolysin fusion. The displayed chain includes the engineered fusion domain; it is not a complete native receptor.", "title": "Structure of the D2 Dopamine Receptor Bound to the Atypical Antipsychotic Drug Risperidone", "resolution": 2.867, "method": "X-RAY DIFFRACTION", "source": "https://www.rcsb.org/structure/6CM4", "sha256": "4ef8156b7a0ce71b4c012b8979b6f1ec051173456c4322c329a338393e534daa", "retrieved": "2026-10-21", "sequenceType": "Deposited protein construct", "sequences": [ { "chain": "A", "authorChain": "A", "name": "D(2) dopamine receptor, endolysin chimera", "sequence": "NYYATLLTLLIAVIVFGNVLVCMAVSREKALQTTTNYLIVSLAVADLLVATLVMPWVVYLEVVGEWKFSRIHCDIFVTLDVMMCTASALNLCAISIDRYTAVAMPMLYNTRYSSKRRVTVMISIVWVLSFTISCPLLFGLNNADQNECIIANPAFVVYSSIVSFYVPFIVTLLVYIKIYIVLRRRRKRNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKLSQQKEKKATQMAAIVAGVFIICWLPFFITHILNIHCDCNIPPVLYSAFTWLGYVNSAVNPIIYTTFNIEFRKAFLKILHC", "length": 430 } ], "citation": { "country": "UK", "id": "primary", "journal_abbrev": "Nature", "journal_id_ASTM": "NATUAS", "journal_id_CSD": "0006", "journal_id_ISSN": "1476-4687", "journal_volume": "555", "page_first": "269", "page_last": "273", "pdbx_database_id_DOI": "10.1038/nature25758", "pdbx_database_id_PubMed": 29466326, "rcsb_ORCID_identifiers": [ "?", "?", "?", "?", "?", "?" ], "rcsb_authors": [ "Wang, S.", "Che, T.", "Levit, A.", "Shoichet, B.K.", "Wacker, D.", "Roth, B.L." ], "rcsb_journal_abbrev": "Nature", "title": "Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone.", "year": 2018 }, "depositedLigands": [ { "id": "8NU", "name": "3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one" }, { "id": "PEG", "name": "DI(HYDROXYETHYL)ETHER" }, { "id": "OLA", "name": "OLEIC ACID" } ] }, { "id": "NMDA", "pdb": "9IYQ", "name": "NMDA receptor", "context": "Learning & memory · synaptic plasticity", "genes": [ "GRIN1", "GRIN2B" ], "geneIds": [ 2902, 2904 ], "chains": [ "A", "B", "C", "D" ], "ligands": [ "GLY", "7RC" ], "contextChains": [], "note": "Human GluN1/GluN2B receptor in the Mg²⁺-free experimental state, with glycine and the antagonist 7RC. This is one NMDA receptor subtype in a specific ligand-bound state. Unresolved and truncated regions are absent from the coordinates.", "title": "Structure of the human GluN1-N2B NMDA receptors in the Mg2+ free state", "resolution": 3.18, "method": "ELECTRON MICROSCOPY", "source": "https://www.rcsb.org/structure/9IYQ", "sha256": "ed7a363d615476ca41fb7158e55de9e59775fd9488bcce42eaf3be87485f59ca", "retrieved": "2026-10-21", "sequenceType": "Deposited protein construct", "sequences": [ { "chain": "A", "authorChain": "A", "name": "Glutamate receptor ionotropic, NMDA 1", "sequence": "MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQ", "length": 847 }, { "chain": "C", "authorChain": "C", "name": "Glutamate receptor ionotropic, NMDA 1", "sequence": "MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQ", "length": 847 }, { "chain": "B", "authorChain": "B", "name": "Glutamate receptor ionotropic, NMDA 2B", "sequence": "MKPRAECCSPKFWLVLAVLAVSGSRARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEHLF", "length": 842 }, { "chain": "D", "authorChain": "D", "name": "Glutamate receptor ionotropic, NMDA 2B", "sequence": "MKPRAECCSPKFWLVLAVLAVSGSRARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEHLF", "length": 842 } ], "citation": { "country": "US", "id": "primary", "journal_abbrev": "Neuron", "journal_id_ASTM": "NERNET", "journal_id_CSD": "2038", "journal_id_ISSN": "0896-6273", "journal_volume": "113", "page_first": "1006", "pdbx_database_id_DOI": "10.1016/j.neuron.2025.01.021", "pdbx_database_id_PubMed": 40010346, "rcsb_ORCID_identifiers": [ "?", "?", "?", "?", "?", "?", "?" ], "rcsb_authors": [ "Huang, X.", "Sun, X.", "Wang, Q.", "Zhang, J.", "Wen, H.", "Chen, W.J.", "Zhu, S." ], "rcsb_journal_abbrev": "Neuron", "title": "Structural insights into the diverse actions of magnesium on NMDA receptors.", "year": 2025 }, "depositedLigands": [ { "id": "GLY", "name": "GLYCINE" }, { "id": "NAG", "name": "2-acetamido-2-deoxy-beta-D-glucopyranose" }, { "id": "7RC", "name": "(2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid" } ] }, { "id": "IL6", "pdb": "1ALU", "name": "Interleukin-6", "context": "Cytokine signalling", "genes": [ "IL6" ], "geneIds": [ 3569 ], "chains": [ "A" ], "ligands": [], "contextChains": [], "note": "Crystal structure of human interleukin-6. The deposited model represents the cytokine; it does not include its receptor complex.", "title": "HUMAN INTERLEUKIN-6", "resolution": 1.9, "method": "X-RAY DIFFRACTION", "source": "https://www.rcsb.org/structure/1ALU", "sha256": "2b3f9bf4c873316e8d6300941dd0f741cda37b9104f6e4e7acb47255e824c03e", "retrieved": "2026-10-21", "sequenceType": "Deposited protein construct", "sequences": [ { "chain": "A", "authorChain": "A", "name": "INTERLEUKIN-6", "sequence": "MAPVPPGEDSKDVAAPHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM", "length": 186 } ], "citation": { "country": "UK", "id": "primary", "journal_abbrev": "EMBO J.", "journal_id_ASTM": "EMJODG", "journal_id_CSD": "0897", "journal_id_ISSN": "0261-4189", "journal_volume": "16", "page_first": "989", "page_last": "997", "pdbx_database_id_DOI": "10.1093/emboj/16.5.989", "pdbx_database_id_PubMed": 9118960, "rcsb_ORCID_identifiers": [ "?", "?", "?" ], "rcsb_authors": [ "Somers, W.", "Stahl, M.", "Seehra, J.S." ], "rcsb_journal_abbrev": "EMBO J", "title": "1.9 A crystal structure of interleukin 6: implications for a novel mode of receptor dimerization and signaling.", "year": 1997 }, "depositedLigands": [ { "id": "SO4", "name": "SULFATE ION" }, { "id": "TLA", "name": "L(+)-TARTARIC ACID" } ] }, { "id": "NR3C1", "pdb": "1M2Z", "name": "Glucocorticoid receptor", "context": "Glucocorticoid signalling", "genes": [ "NR3C1" ], "geneIds": [ 2908 ], "chains": [ "A", "C" ], "ligands": [ "DEX" ], "contextChains": [ "B", "D" ], "note": "Ligand-binding domains with dexamethasone and TIF2 coactivator motifs. This partial, engineered construct does not contain the full glucocorticoid receptor or its DNA-binding domain.", "title": "Crystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding domain bound to dexamethasone and a TIF2 coactivator motif", "resolution": 2.5, "method": "X-RAY DIFFRACTION", "source": "https://www.rcsb.org/structure/1M2Z", "sha256": "b85290f126ed2220beb5907b59d9311239a8a9e79d4ad28ff6da7328b445bd10", "retrieved": "2026-10-21", "sequenceType": "Deposited protein construct", "sequences": [ { "chain": "A", "authorChain": "A", "name": "glucocorticoid receptor", "sequence": "VPATLPQLTPTLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQK", "length": 257 }, { "chain": "C", "authorChain": "D", "name": "glucocorticoid receptor", "sequence": "VPATLPQLTPTLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQK", "length": 257 } ], "citation": { "country": "US", "id": "primary", "journal_abbrev": "Cell(Cambridge,Mass.)", "journal_id_ASTM": "CELLB5", "journal_id_CSD": "0998", "journal_id_ISSN": "0092-8674", "journal_volume": "110", "page_first": "93", "page_last": "105", "pdbx_database_id_DOI": "10.1016/S0092-8674(02)00817-6", "pdbx_database_id_PubMed": 12151000, "rcsb_ORCID_identifiers": [ "?", "?", "?", "?", "?", "?", "?", "?", "?", "?", "?", "?", "?", "?" ], "rcsb_authors": [ "Bledsoe, R.B.", "Montana, V.G.", "Stanley, T.B.", "Delves, C.J.", "Apolito, C.J.", "Mckee, D.D.", "Consler, T.G.", "Parks, D.J.", "Stewart, E.L.", "Willson, T.M.", "Lambert, M.H.", "Moore, J.T.", "Pearce, K.H.", "Xu, H.E." ], "rcsb_journal_abbrev": "Cell", "title": "Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Reveals a Novel Mode of Receptor Dimerization and Coactivator Recognition", "year": 2002 }, "depositedLigands": [ { "id": "BOG", "name": "octyl beta-D-glucopyranoside" }, { "id": "DEX", "name": "DEXAMETHASONE" } ] }, { "id": "DOCK2", "pdb": "6TGB", "name": "Dedicator of cytokinesis 2", "context": "RAC activation · immune-cell migration", "genes": [ "DOCK2" ], "geneIds": [ 1794 ], "chains": [ "A", "C" ], "ligands": [], "contextChains": [ "B" ], "note": "DOCK2 from the deposited DOCK2–ELMO1 complex. ELMO1 is available in the complex layer. At 5.50 Å resolution, fine atomic details require cautious interpretation.", "title": "CryoEM structure of the binary DOCK2-ELMO1 complex", "resolution": 5.5, "method": "ELECTRON MICROSCOPY", "source": "https://www.rcsb.org/structure/6TGB", "sha256": "6a42f297e03f533faa40bc6f5bbec85024395b3391c37634e38067deaec0d367", "retrieved": "2026-10-21", "sequenceType": "Deposited protein construct", "sequences": [ { "chain": "A", "authorChain": "A", "name": "Dedicator of cytokinesis protein 2", "sequence": "MAPWRKADKERHGVAIYNFQGSGAPQLSLQIGDVVRIQETCGDWYRGYLIKHKMLQGIFPKSFIHIKEVTVEKRRNTENIIPAEIPLAQEVTTTLWEWGSIWKQLYVASKKERFLQVQSMMYDLMEWRSQLLSGTLPKDELKELKQKVTSKIDYGNKILELDLIVRDEDGNILDPDNTSVISLFHAHEEATDKITERIKEEMSKDQPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGFPEIIMPGDVRNDIYITLLQGDFDKYNKTTQRNVEVIMCVCAEDGKTLPNAICVGAGDKPMNEYRSVVYYQVKQPRWMETVKVAVPIEDMQRIHLRFMFRHRSSLESKDKGEKNFAMSYVKLMKEDGTTLHDGFHDLVVLKGDSKKMEDASAYLTLPSYRHHVENKGATLSRSSSSVGGLSVSSRDVFSISTLVCSTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIMMEHSQSDEYDILVFDALIYIIGLIADRKFQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSSELVDFLMETFIMFKDLIGKNVYPGDWMAMSMVQNRVFLRAINKFAETMNQKFLEHTNFEFQLWNNYFHLAVAFITQDSLQLEQFSHAKYNKILNKYGDMRRLIGFSIRDMWYKLGQNKICFIPGMVGPILEMTLIPEAELRKATIPIFFDMMLCEYQRSGDFKKFENEIILKLDHEVEGGRGDEQYMQLLESILMECAAEHPTIAKSVENFVNLVKGLLEKLLDYRGVMTDESKDNRMSCTVNLLNFYKDNNREEMYIRYLYKLRDLHLDCDNYTEAAYTLLLHTWLLKWSDEQCASQVMQTGQQHPQTHRQLKETLYETIIGYFDKGKMWEEAISLCKELAEQYEMEIFDYELLSQNLIQQAKFYESIMKILRPKPDYFAVGYYGQGFPSFLRNKVFIYRGKEYERREDFQMQLMTQFPNAEKMNTTSAPGDDVKNAPGQYIQCFTVQPVLDEHPRFKNKPVPDQIINFYKSNYVQRFHYSRPVRRGTVDPENEFASMWIERTSFVTAYKLPGILRWFEVVHMSQTTISPLENAIETMSTANEKILMMINQYQSDETLPINPLSMLLNGIVDPAVMGGFAKYEKAFFTEEYVRDHPEDQDKLTHLKDLIAWQIPFLGAGIKIHEKRVSDNLRPFHDRMEECFKNLKMKVEKEYGVREMPDFDDRRVGRPRSMLRSYRQMSIISLASMNSDCSTPSKPTSESFDLELASPKTPRVEQEEPISPGSTLPEVKLRRSKKRTKRSSVVFADEKAAAESDLKRLSRKHEFMSDTNLSEHAAIPLKASVLSQMSFASQSMPTIPALALSVAGIPGLDEANTSPRLSQTFLQLSDGDKKTLTRKKVNQFFKTMLASKSAEEGKQIPDSLSTDL", "length": 1830 }, { "chain": "C", "authorChain": "D", "name": "Dedicator of cytokinesis protein 2", "sequence": "MAPWRKADKERHGVAIYNFQGSGAPQLSLQIGDVVRIQETCGDWYRGYLIKHKMLQGIFPKSFIHIKEVTVEKRRNTENIIPAEIPLAQEVTTTLWEWGSIWKQLYVASKKERFLQVQSMMYDLMEWRSQLLSGTLPKDELKELKQKVTSKIDYGNKILELDLIVRDEDGNILDPDNTSVISLFHAHEEATDKITERIKEEMSKDQPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGFPEIIMPGDVRNDIYITLLQGDFDKYNKTTQRNVEVIMCVCAEDGKTLPNAICVGAGDKPMNEYRSVVYYQVKQPRWMETVKVAVPIEDMQRIHLRFMFRHRSSLESKDKGEKNFAMSYVKLMKEDGTTLHDGFHDLVVLKGDSKKMEDASAYLTLPSYRHHVENKGATLSRSSSSVGGLSVSSRDVFSISTLVCSTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIMMEHSQSDEYDILVFDALIYIIGLIADRKFQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSSELVDFLMETFIMFKDLIGKNVYPGDWMAMSMVQNRVFLRAINKFAETMNQKFLEHTNFEFQLWNNYFHLAVAFITQDSLQLEQFSHAKYNKILNKYGDMRRLIGFSIRDMWYKLGQNKICFIPGMVGPILEMTLIPEAELRKATIPIFFDMMLCEYQRSGDFKKFENEIILKLDHEVEGGRGDEQYMQLLESILMECAAEHPTIAKSVENFVNLVKGLLEKLLDYRGVMTDESKDNRMSCTVNLLNFYKDNNREEMYIRYLYKLRDLHLDCDNYTEAAYTLLLHTWLLKWSDEQCASQVMQTGQQHPQTHRQLKETLYETIIGYFDKGKMWEEAISLCKELAEQYEMEIFDYELLSQNLIQQAKFYESIMKILRPKPDYFAVGYYGQGFPSFLRNKVFIYRGKEYERREDFQMQLMTQFPNAEKMNTTSAPGDDVKNAPGQYIQCFTVQPVLDEHPRFKNKPVPDQIINFYKSNYVQRFHYSRPVRRGTVDPENEFASMWIERTSFVTAYKLPGILRWFEVVHMSQTTISPLENAIETMSTANEKILMMINQYQSDETLPINPLSMLLNGIVDPAVMGGFAKYEKAFFTEEYVRDHPEDQDKLTHLKDLIAWQIPFLGAGIKIHEKRVSDNLRPFHDRMEECFKNLKMKVEKEYGVREMPDFDDRRVGRPRSMLRSYRQMSIISLASMNSDCSTPSKPTSESFDLELASPKTPRVEQEEPISPGSTLPEVKLRRSKKRTKRSSVVFADEKAAAESDLKRLSRKHEFMSDTNLSEHAAIPLKASVLSQMSFASQSMPTIPALALSVAGIPGLDEANTSPRLSQTFLQLSDGDKKTLTRKKVNQFFKTMLASKSAEEGKQIPDSLSTDL", "length": 1830 } ], "citation": { "country": "UK", "id": "primary", "journal_abbrev": "Nat Commun", "journal_id_ISSN": "2041-1723", "journal_volume": "11", "page_first": "3464", "page_last": "3464", "pdbx_database_id_DOI": "10.1038/s41467-020-17271-9", "pdbx_database_id_PubMed": 32651375, "rcsb_ORCID_identifiers": [ "?", "?", "0000-0002-7819-8307", "0000-0003-1218-6714", "0000-0002-7268-9631", "0000-0001-9135-6253", "0000-0002-7848-3327", "?", "0000-0003-2896-9350", "0000-0001-7055-2642", "0000-0001-8810-950X" ], "rcsb_authors": [ "Chang, L.", "Yang, J.", "Jo, C.H.", "Boland, A.", "Zhang, Z.", "McLaughlin, S.H.", "Abu-Thuraia, A.", "Killoran, R.C.", "Smith, M.J.", "Cote, J.F.", "Barford, D." ], "rcsb_journal_abbrev": "Nat Commun", "title": "Structure of the DOCK2-ELMO1 complex provides insights into regulation of the auto-inhibited state.", "year": 2020 }, "depositedLigands": [] }, { "id": "CD38", "pdb": "1YH3", "name": "CD38 extracellular domain", "context": "NAD metabolism · calcium signalling", "genes": [ "CD38" ], "geneIds": [ 952 ], "chains": [ "A" ], "ligands": [], "contextChains": [ "B" ], "note": "Engineered extracellular domain of human CD38. The membrane-spanning region is absent. A second deposited copy is available in the complex layer.", "title": "Crystal structure of human CD38 extracellular domain", "resolution": 1.91, "method": "X-RAY DIFFRACTION", "source": "https://www.rcsb.org/structure/1YH3", "sha256": "067d78c80288a67a7437ccdb7422e67e0a8fbc11288993c09079198b21633632", "retrieved": "2026-10-21", "sequenceType": "Deposited protein construct", "sequences": [ { "chain": "A", "authorChain": "A", "name": "ADP-ribosyl cyclase 1", "sequence": "RWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFATSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI", "length": 256 } ], "citation": { "country": "UK", "id": "primary", "journal_abbrev": "Structure", "journal_id_ASTM": "STRUE6", "journal_id_CSD": "2005", "journal_id_ISSN": "0969-2126", "journal_volume": "13", "page_first": "1331", "page_last": "1339", "pdbx_database_id_DOI": "10.1016/j.str.2005.05.012", "pdbx_database_id_PubMed": 16154090, "rcsb_ORCID_identifiers": [ "?", "?", "?", "?", "?", "?" ], "rcsb_authors": [ "Liu, Q.", "Kriksunov, I.A.", "Graeff, R.", "Munshi, C.", "Lee, H.C.", "Hao, Q." ], "rcsb_journal_abbrev": "Structure", "title": "Crystal structure of human CD38 extracellular domain.", "year": 2005 }, "depositedLigands": [] } ] }, "docking": { "schema": "universal-informatics/oxtr-contact/v1", "pdb": "7QVM", "source": "https://files.rcsb.org/download/7QVM.pdb", "sourceSHA256": "41b57ce550e83d1aa95308d4d8886bcfb9f0608535ce51b842af6376d77661db", "publication": "https://www.nature.com/articles/s41467-022-31325-0", "resolutionAngstrom": 3.25, "ligand": [ { "name": "N", "residue": 1, "comp": "CYS", "chain": "L", "element": "N", "position": [ 140.514, 140.102, 173.553 ] }, { "name": "CA", "residue": 1, "comp": "CYS", "chain": "L", "element": "C", "position": [ 141.737, 140.494, 172.801 ] }, { "name": "C", "residue": 1, "comp": "CYS", "chain": "L", "element": "C", "position": [ 141.349, 140.943, 171.388 ] }, { "name": "O", "residue": 1, "comp": "CYS", "chain": "L", "element": "O", "position": [ 142.093, 141.757, 170.807 ] }, { "name": "CB", "residue": 1, "comp": "CYS", "chain": "L", "element": "C", "position": [ 142.726, 139.336, 172.72 ] }, { "name": "SG", "residue": 1, "comp": "CYS", "chain": "L", "element": "S", "position": [ 143.493, 138.927, 174.31 ] }, { "name": "N", "residue": 2, "comp": "TYR", "chain": "L", "element": "N", "position": [ 140.233, 140.431, 170.862 ] }, { "name": "CA", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 139.755, 140.855, 169.519 ] }, { "name": "C", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 138.712, 141.966, 169.686 ] }, { "name": "O", "residue": 2, "comp": "TYR", "chain": "L", "element": "O", "position": [ 138.754, 142.939, 168.91 ] }, { "name": "CB", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 139.228, 139.65, 168.735 ] }, { "name": "CG", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 140.278, 138.611, 168.433 ] }, { "name": "CD1", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 141.423, 138.942, 167.727 ] }, { "name": "CD2", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 140.132, 137.3, 168.853 ] }, { "name": "CE1", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 142.394, 137.997, 167.442 ] }, { "name": "CE2", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 141.094, 136.343, 168.577 ] }, { "name": "CZ", "residue": 2, "comp": "TYR", "chain": "L", "element": "C", "position": [ 142.229, 136.692, 167.869 ] }, { "name": "OH", "residue": 2, "comp": "TYR", "chain": "L", "element": "O", "position": [ 143.183, 135.756, 167.593 ] }, { "name": "N", "residue": 3, "comp": "ILE", "chain": "L", "element": "N", "position": [ 137.811, 141.826, 170.664 ] }, { "name": "CA", "residue": 3, "comp": "ILE", "chain": "L", "element": "C", "position": [ 136.82, 142.908, 170.953 ] }, { "name": "C", "residue": 3, "comp": "ILE", "chain": "L", "element": "C", "position": [ 136.784, 143.121, 172.468 ] }, { "name": "O", "residue": 3, "comp": "ILE", "chain": "L", "element": "O", "position": [ 135.815, 143.735, 172.954 ] }, { "name": "CB", "residue": 3, "comp": "ILE", "chain": "L", "element": "C", "position": [ 135.427, 142.573, 170.381 ] }, { "name": "CG1", "residue": 3, "comp": "ILE", "chain": "L", "element": "C", "position": [ 134.808, 141.349, 171.061 ] }, { "name": "CG2", "residue": 3, "comp": "ILE", "chain": "L", "element": "C", "position": [ 135.486, 142.41, 168.87 ] }, { "name": "CD1", "residue": 3, "comp": "ILE", "chain": "L", "element": "C", "position": [ 133.402, 141.043, 170.599 ] }, { "name": "N", "residue": 4, "comp": "GLN", "chain": "L", "element": "N", "position": [ 137.805, 142.634, 173.18 ] }, { "name": "CA", "residue": 4, "comp": "GLN", "chain": "L", "element": "C", "position": [ 137.871, 142.787, 174.626 ] }, { "name": "C", "residue": 4, "comp": "GLN", "chain": "L", "element": "C", "position": [ 139.333, 142.985, 175.005 ] }, { "name": "O", "residue": 4, "comp": "GLN", "chain": "L", "element": "O", "position": [ 140.219, 142.994, 174.148 ] }, { "name": "CB", "residue": 4, "comp": "GLN", "chain": "L", "element": "C", "position": [ 137.258, 141.575, 175.339 ] }, { "name": "CG", "residue": 4, "comp": "GLN", "chain": "L", "element": "C", "position": [ 136.785, 141.84, 176.762 ] }, { "name": "CD", "residue": 4, "comp": "GLN", "chain": "L", "element": "C", "position": [ 136.217, 140.602, 177.427 ] }, { "name": "OE1", "residue": 4, "comp": "GLN", "chain": "L", "element": "O", "position": [ 136.335, 139.494, 176.905 ] }, { "name": "NE2", "residue": 4, "comp": "GLN", "chain": "L", "element": "N", "position": [ 135.592, 140.786, 178.583 ] }, { "name": "N", "residue": 5, "comp": "ASN", "chain": "L", "element": "N", "position": [ 139.574, 143.162, 176.3 ] }, { "name": "CA", "residue": 5, "comp": "ASN", "chain": "L", "element": "C", "position": [ 140.927, 143.361, 176.798 ] }, { "name": "C", "residue": 5, "comp": "ASN", "chain": "L", "element": "C", "position": [ 141.565, 142.035, 177.195 ] }, { "name": "O", "residue": 5, "comp": "ASN", "chain": "L", "element": "O", "position": [ 140.914, 141.162, 177.776 ] }, { "name": "CB", "residue": 5, "comp": "ASN", "chain": "L", "element": "C", "position": [ 140.918, 144.318, 177.991 ] }, { "name": "CG", "residue": 5, "comp": "ASN", "chain": "L", "element": "C", "position": [ 139.865, 143.957, 179.023 ] }, { "name": "OD1", "residue": 5, "comp": "ASN", "chain": "L", "element": "O", "position": [ 139.134, 142.979, 178.869 ] }, { "name": "ND2", "residue": 5, "comp": "ASN", "chain": "L", "element": "N", "position": [ 139.783, 144.75, 180.085 ] }, { "name": "N", "residue": 6, "comp": "CYS", "chain": "L", "element": "N", "position": [ 142.843, 141.87, 176.846 ] }, { "name": "CA", "residue": 6, "comp": "CYS", "chain": "L", "element": "C", "position": [ 143.56, 140.607, 177.168 ] }, { "name": "C", "residue": 6, "comp": "CYS", "chain": "L", "element": "C", "position": [ 143.778, 140.518, 178.681 ] }, { "name": "O", "residue": 6, "comp": "CYS", "chain": "L", "element": "O", "position": [ 144.309, 141.487, 179.258 ] }, { "name": "CB", "residue": 6, "comp": "CYS", "chain": "L", "element": "C", "position": [ 144.906, 140.553, 176.458 ] }, { "name": "SG", "residue": 6, "comp": "CYS", "chain": "L", "element": "S", "position": [ 144.763, 140.478, 174.653 ] }, { "name": "N", "residue": 7, "comp": "PRO", "chain": "L", "element": "N", "position": [ 143.399, 139.405, 179.345 ] }, { "name": "CA", "residue": 7, "comp": "PRO", "chain": "L", "element": "C", "position": [ 143.645, 139.245, 180.778 ] }, { "name": "C", "residue": 7, "comp": "PRO", "chain": "L", "element": "C", "position": [ 145.155, 139.243, 181.054 ] }, { "name": "O", "residue": 7, "comp": "PRO", 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147.737, 137.219, 181.379 ] }, { "name": "CG", "residue": 8, "comp": "LEU", "chain": "L", "element": "C", "position": [ 147.315, 137.384, 182.839 ] }, { "name": "CD1", "residue": 8, "comp": "LEU", "chain": "L", "element": "C", "position": [ 147.622, 136.128, 183.64 ] }, { "name": "CD2", "residue": 8, "comp": "LEU", "chain": "L", "element": "C", "position": [ 147.994, 138.592, 183.464 ] }, { "name": "N", "residue": 9, "comp": "GLY", "chain": "L", "element": "N", "position": [ 147.57, 138.98, 178.083 ] }, { "name": "CA", "residue": 9, "comp": "GLY", "chain": "L", "element": "C", "position": [ 148.143, 138.901, 176.725 ] }, { "name": "C", "residue": 9, "comp": "GLY", "chain": "L", "element": "C", "position": [ 148.107, 137.483, 176.181 ] }, { "name": "O", "residue": 9, "comp": "GLY", "chain": "L", "element": "O", "position": [ 149.109, 137.058, 175.573 ] }, { "name": "N", "residue": 10, "comp": "NH2", "chain": "L", "element": "N", "position": [ 146.992, 136.777, 176.394 ] } ], "pocket": [ { "name": "N", "residue": 92, "comp": "GLN", "chain": "R", "element": "N", "position": [ 143.978, 139.487, 161.309 ] }, { "name": "CA", "residue": 92, "comp": "GLN", "chain": "R", "element": "C", "position": [ 143.49, 138.941, 162.607 ] }, { "name": "C", "residue": 92, "comp": "GLN", "chain": "R", "element": "C", "position": [ 144.628, 138.397, 163.471 ] }, { "name": "O", "residue": 92, "comp": "GLN", "chain": "R", "element": "O", "position": [ 144.75, 138.853, 164.624 ] }, { "name": "CB", "residue": 92, "comp": "GLN", "chain": "R", "element": "C", "position": [ 142.457, 137.838, 162.366 ] }, { "name": "CG", "residue": 92, "comp": "GLN", "chain": "R", "element": "C", "position": [ 141.763, 137.368, 163.636 ] }, { "name": "CD", "residue": 92, "comp": "GLN", "chain": "R", "element": "C", "position": [ 140.839, 138.414, 164.211 ] }, { "name": "OE1", "residue": 92, "comp": "GLN", "chain": "R", "element": "O", "position": [ 140.798, 139.555, 163.758 ] }, { "name": "NE2", "residue": 92, "comp": "GLN", "chain": "R", "element": "N", "position": [ 140.074, 138.023, 165.218 ] }, { "name": "N", "residue": 171, "comp": "GLN", "chain": "R", "element": "N", "position": [ 132.298, 148.951, 167.132 ] }, { "name": "CA", "residue": 171, "comp": "GLN", "chain": "R", "element": "C", "position": [ 133.509, 148.447, 167.831 ] }, { "name": "C", "residue": 171, "comp": "GLN", "chain": "R", "element": "C", "position": [ 134.442, 149.627, 168.105 ] }, { "name": "O", "residue": 171, "comp": "GLN", "chain": "R", "element": "O", "position": [ 134.785, 149.848, 169.283 ] }, { "name": "CB", "residue": 171, "comp": "GLN", "chain": "R", "element": "C", "position": [ 134.211, 147.397, 166.97 ] }, { "name": "CG", "residue": 171, "comp": "GLN", "chain": "R", "element": "C", "position": [ 135.62, 147.06, 167.438 ] }, { "name": "CD", "residue": 171, "comp": "GLN", "chain": "R", "element": "C", "position": [ 135.637, 146.167, 168.655 ] }, { "name": "OE1", "residue": 171, "comp": "GLN", "chain": "R", "element": "O", "position": [ 134.607, 145.888, 169.263 ] }, { "name": "NE2", "residue": 171, "comp": "GLN", "chain": "R", "element": "N", "position": [ 136.823, 145.706, 169.017 ] }, { "name": "N", "residue": 291, "comp": "PHE", "chain": "R", "element": "N", "position": [ 135.7, 130.127, 172.01 ] }, { "name": "CA", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 135.969, 131.585, 172.102 ] }, { "name": "C", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 134.762, 132.304, 172.709 ] }, { "name": "O", "residue": 291, "comp": "PHE", "chain": "R", "element": "O", "position": [ 134.952, 133.066, 173.675 ] }, { "name": "CB", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 136.301, 132.162, 170.725 ] }, { "name": "CG", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 136.497, 133.657, 170.713 ] }, { "name": "CD1", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 137.729, 134.212, 171.019 ] }, { "name": "CD2", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 135.448, 134.509, 170.407 ] }, { "name": "CE1", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 137.909, 135.586, 171.012 ] }, { "name": "CE2", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 135.629, 135.882, 170.402 ] }, { "name": "CZ", "residue": 291, "comp": "PHE", "chain": "R", "element": "C", "position": [ 136.858, 136.419, 170.704 ] }, { "name": "N", "residue": 316, "comp": "LEU", "chain": "R", "element": "N", "position": [ 142.678, 133.525, 172.821 ] }, { "name": "CA", "residue": 316, "comp": "LEU", "chain": "R", "element": "C", "position": [ 143.176, 134.007, 171.501 ] }, { "name": "C", "residue": 316, "comp": "LEU", "chain": "R", "element": "C", "position": [ 142.66, 133.132, 170.353 ] }, { "name": "O", "residue": 316, "comp": "LEU", "chain": "R", "element": "O", "position": [ 142.608, 133.644, 169.219 ] }, { "name": "CB", "residue": 316, "comp": "LEU", "chain": "R", "element": "C", "position": [ 144.709, 134.004, 171.527 ] }, { "name": "CG", "residue": 316, "comp": "LEU", "chain": "R", "element": "C", "position": [ 145.367, 135.157, 172.284 ] }, { "name": "CD1", "residue": 316, "comp": "LEU", "chain": "R", "element": "C", "position": [ 145.007, 135.124, 173.762 ] }, { "name": "CD2", "residue": 316, "comp": "LEU", "chain": "R", "element": "C", "position": [ 146.877, 135.123, 172.109 ] } ], "rings": [ { "points": [ [ 140.278, 138.611, 168.433 ], [ 141.423, 138.942, 167.727 ], [ 142.394, 137.997, 167.442 ], [ 142.229, 136.692, 167.869 ], [ 141.094, 136.343, 168.577 ], [ 140.132, 137.3, 168.853 ] ], "center": [ 141.25833333333335, 137.6475, 168.15016666666668 ], "normal": [ 0.465847109820904, 0.2214777496721545, 0.8566995253130876 ] }, { "points": [ [ 136.497, 133.657, 170.713 ], [ 137.729, 134.212, 171.019 ], [ 137.909, 135.586, 171.012 ], [ 136.858, 136.419, 170.704 ], [ 135.629, 135.882, 170.402 ], [ 135.448, 134.509, 170.407 ] ], "center": [ 136.6783333333333, 135.04416666666668, 170.70949999999996 ], "normal": [ -0.2541566622094789, 0.03678000753453492, 0.9664634613374147 ] } ], "receptorCenter": [ 135.53389117352071, 134.10806068204627, 161.9040902708125 ], "ligandCenter": [ 141.70179710144927, 140.24759420289857, 175.25566666666666 ], "approachVector": [ 9.675191855132192, 9.630685910154698, 20.943747311938505 ], "hydrogenBond": [ [ 143.183, 135.756, 167.593 ], [ 142.608, 133.644, 169.219 ] ], "measurements": { "centroidDistanceAngstrom": 5.8569558266693145, "ringPlaneAngleDegrees": 44.13372131618806, "closestRingCarbonAngstrom": 3.5413000437692395, "hydrogenBondHeavyAtomDistanceAngstrom": 2.7267278925481326 }, "interpretation": "Deposited bound pose. Interpolated approach is illustrative, not a calculated binding trajectory. Aromatic contact is not classified as a parallel pi stack. No affinity or activation prediction." }, "calculated_orbitals": { "schema": "universal-informatics/quantum-fragment/v1", "software": "PySCF 2.14.0", "method": "PBE0 / def2-SVP", "densityFitting": true, "gridLevel": 3, "scfConverged": true, "convergenceToleranceHartree": 1e-09, "totalEnergyHartree": -617.172473610136, "electrons": 108, "charge": 0, "spin": 0, "atoms": [ { "element": "C", "position": [ -2.9110593449956235, 0.0047819159459252525, -0.0005877208557849567 ], "name": "CB", "group": "Tyr2" }, { "element": "C", "position": [ -1.4033459663835248, -0.00025435688840397264, -0.0006502511557356649 ], "name": "CG", "group": "Tyr2" }, { "element": "C", "position": [ -0.688667923861174, 1.1864445934857415, 0.0010517233863508446 ], "name": "CD1", "group": "Tyr2" }, { "element": "C", "position": [ 0.695892522708559, 1.1954591135605457, -0.0004002485262292188 ], "name": "CE1", "group": "Tyr2" }, { "element": "C", "position": [ 1.390765341349224, -0.0002543568884041669, -0.0006502511557356649 ], "name": "CZ", "group": "Tyr2" }, { "element": "C", "position": [ 0.6950285628536534, -1.1949258072765014, 2.8480204892711303e-05 ], "name": "CE2", "group": "Tyr2" }, { "element": "C", "position": [ -0.6896725366667857, -1.186469185993032, 0.0006205472463490791 ], "name": "CD2", "group": "Tyr2" }, { "element": "O", "position": [ 2.75545757442067, 0.0014763707222420486, -0.0003132401936421503 ], "name": "OH", "group": "Tyr2" }, { "element": "H", "position": [ -1.2308355281593835, 2.120496842175082, 0.0018797136687598304 ], "name": "HCD1", "group": "Tyr2" }, { "element": "H", "position": [ 1.2392232702388166, 2.128835565551455, -0.0007127498448427083 ], "name": "HCE1", "group": "Tyr2" }, { "element": "H", "position": [ 1.2380363029906782, -2.128490263356638, 5.0731048282792734e-05 ], "name": "HCE2", "group": "Tyr2" }, { "element": "H", "position": [ -1.2324230955084272, -2.120183056721242, 0.0011088983794471652 ], "name": "HCD2", "group": "Tyr2" }, { "element": "H", "position": [ -3.274348027898748, 0.005996250354853405, 1.0270892022413904 ], "name": "HC1", "group": "Tyr2" }, { "element": "H", "position": [ -3.2773847845555326, -0.8839810851194225, -0.5144028629726521 ], "name": "HC2", "group": "Tyr2" }, { "element": "H", "position": [ -3.271439140612169, 0.8959715310989889, -0.5144042958655183 ], "name": "HC3", "group": "Tyr2" }, { "element": "H", "position": [ 3.0532715418968808, -0.9111609260446426, -0.0002402599837343644 ], "name": "HO", "group": "Tyr2" }, { "element": "C", "position": [ -0.21376701482169402, -7.714392163799808, -1.3183656278517106 ], "name": "CB", "group": "Phe291" }, { "element": "C", "position": [ -1.1012552809967757, -6.567257442485251, -0.9060168573234773 ], "name": "CG", "group": "Phe291" }, { "element": "C", "position": [ -0.6839479973631067, -5.658487248433028, 0.052876445097890024 ], "name": "CD1", "group": "Phe291" }, { "element": "C", "position": [ -1.5005146078935292, -4.606183751716874, 0.43523925888326787 ], "name": "CE1", "group": "Phe291" }, { "element": "C", "position": [ -2.744314735104637, -4.454788559420242, -0.13343880408299835 ], "name": "CZ", "group": "Phe291" }, { "element": "C", "position": [ -3.1726970964971373, -5.351366011284566, -1.0835184982436061 ], "name": "CE2", "group": "Phe291" }, { "element": "C", "position": [ -2.357111835561643, -6.402571773249482, -1.4678388439925545 ], "name": "CD2", "group": "Phe291" }, { "element": "H", "position": [ 0.2917260252645386, -5.777600343390793, 0.5003943466160177 ], "name": "HCD1", "group": "Phe291" }, { "element": "H", "position": [ -1.1666065365715572, -3.9004882545517523, 1.181496094823078 ], "name": "HCE1", "group": "Phe291" }, { "element": "H", "position": [ -4.149612201615947, -5.229523922452531, -1.5275808618590612 ], "name": "HCE2", "group": "Phe291" }, { "element": "H", "position": [ -2.6951378866030526, -7.105991911884666, -2.214389912158569 ], "name": "HCD2", "group": "Phe291" }, { "element": "H", "position": [ -3.381218203981736, -3.635374060354028, 0.16541542468481696 ], "name": "HCZ", "group": "Phe291" }, { "element": "H", "position": [ -0.4113114205848366, -8.574682936585488, -0.6788533183443008 ], "name": "HC1", "group": "Phe291" }, { "element": "H", "position": [ 0.8308720010460705, -7.4196796944709575, -1.218496278454908 ], "name": "HC2", "group": "Phe291" }, { "element": "H", "position": [ -0.4193071773559843, -7.978063564785253, -2.355829185711814 ], "name": "HC3", "group": "Phe291" } ], "orbitals": [ { "id": "homo-minus-1", "index": 53, "energyEV": -7.1031849597193, "occupation": 2.0, "file": "homo-minus-1.cube", "min": -0.21426538660457028, "max": 0.21950498657705256 }, { "id": "homo", "index": 54, "energyEV": -6.177474573284318, "occupation": 2.0, "file": "homo.cube", "min": -0.28037254852972066, "max": 0.263746907881252 }, { "id": "lumo", "index": 55, "energyEV": -0.1414146849892533, "occupation": 0.0, "file": "lumo.cube", "min": -0.200981036825699, "max": 0.20631021746841408 } ], "gridSpacingBohr": 0.38, "cubeLengthUnit": "Bohr", "orbitalUnit": "Bohr^(-3/2)", "densityUnit": "electrons / Bohr^3", "sourcePDB": "7QVM", "sourceSHA256": "41b57ce550e83d1aa95308d4d8886bcfb9f0608535ce51b842af6376d77661db", "fragmentSHA256": "c9445c2d800c0b01d12b65ea6b670f21165d9750adbaecb6d32352afa101d9cf", "model": "Neutral p-cresol and toluene pair representing capped Tyr2 and Phe291 side chains.", "preparation": "Deposited heavy atoms fixed; beta-carbon bonds to the omitted backbone replaced by methyl hydrogens. Aromatic and hydroxyl hydrogens added at idealised geometry. No optimisation.", "environment": "Gas phase; no protein embedding, water, membrane or ions.", "interpretation": "Stationary single-point electronic model. Orbitals are wavefunctions, not electron trajectories. Orbital signs are not electrical charges. This fragment model does not predict binding affinity or receptor activation.", "limitations": "Results depend on capping, proton orientation, basis and density functional. No time-dependent response or biological validation. The visualization grid undersamples core-density peaks and is not an electron-count integration grid.", "references": [ "https://www.rcsb.org/structure/7QVM", "https://www.nature.com/articles/s41467-022-31325-0", "https://pyscf.org/user/dft.html" ], "files": { "homo-minus-1.cube": "76e110eef447e98007c43ac3de8a8451fa0b3e59657ed87a069244ebfb182d64", "density.cube": "e35efe317f9fbddbdb003567f3d950268e8e00019a34acb18d85d8c96b037f0a", "homo.cube": "2d4f4a177f6a3ec352afa15c1a26e14f456e706afe0b0e2701d58b22223a5b8d", "lumo.cube": "ce88117e7e8fba07f4bc38cca2599b084734c550ed0d6d757c5d2c596150c3f0" } } } ``` ## Sources - [molecular/index.html](https://universalmind.tv/informatics/molecular/index.html) · SHA-256: 7c0c8fadb9cb7a1c108de2d2e4777d28af473115be318e311d3a983bb607953f · Exact file bytes - [molecular/interaction-ui.js](https://universalmind.tv/informatics/molecular/interaction-ui.js) · SHA-256: bfa28324268e2be47f6e4eb0f4250270b8846b37013f4eb78eed6bf255d86d6e · Exact file bytes - [molecular/data/catalogue.json](https://universalmind.tv/informatics/molecular/data/catalogue.json) · SHA-256: 52fe47c82c28997bd15ba7ed59e8643125546fa38242d80f6c7d7c8da597c04c · Exact file bytes