Structure of PDB 6wm3 Chain E Binding Site BS01

Receptor Information
>6wm3 Chain E (length=468) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGTKRSGQVLE
VSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKP
IDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQK
IPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNM
ETARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQ
CEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERA
GRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQI
YPPINVLPSLSRLMKSAIGEGMTRKDHADVSNQLYACYAIGKDVQAMKAV
VGEEALTSDDLLYLEFLQKFERNFIAQGPYENRTVFETLDIGWQLLRIFP
KEMLKRIPQSTLSEFYPR
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6wm3 Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6wm3 Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		R400 K403
Binding residue
(residue number reindexed from 1)		R362 K365
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H199 V236 N237 R400
Catalytic site (residue number reindexed from 1) H161 V198 N199 R362
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0015078 proton transmembrane transporter activity
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0007035 vacuolar acidification
GO:0016241 regulation of macroautophagy
GO:0046034 ATP metabolic process
GO:0097401 synaptic vesicle lumen acidification
GO:1902600 proton transmembrane transport
Cellular Component
GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain
GO:0001726 ruffle
GO:0005737 cytoplasm
GO:0005765 lysosomal membrane
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005902 microvillus
GO:0016324 apical plasma membrane
GO:0016469 proton-transporting two-sector ATPase complex
GO:0030665 clathrin-coated vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031090 organelle membrane
GO:0031410 cytoplasmic vesicle
GO:0033180 proton-transporting V-type ATPase, V1 domain
GO:0042470 melanosome
GO:0043231 intracellular membrane-bounded organelle
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:0098850 extrinsic component of synaptic vesicle membrane

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6wm3, PDBe:6wm3, PDBj:6wm3
PDBsum6wm3
PubMed33065002
UniProtP21281|VATB2_HUMAN V-type proton ATPase subunit B, brain isoform (Gene Name=ATP6V1B2)

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