Structure of PDB 6wm3 Chain B Binding Site BS01

Receptor Information
>6wm3 Chain B (length=600) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQV
YEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSI
YIPRGVNVSALSRDIKWDFTPCKNLRVGSHITGGDIYGIVSENSLIKHKI
MLPPRNRGTVTYIAPPGNYDTSDVVLELEFEGVKEKFTMVQVWPVRQVRP
VTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKY
SNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTS
NMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLA
EMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGD
FSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYD
KHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIK
DDFLQQNGYTPYDRFCPFYKTVGMLSNMIAFYDMARRAVETTAQSDNKIT
WSIIREHMGDILYKLSSMKFKDPLKDGEAKIKSDYAQLLEDMQNAFRSLE
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)		G253 G255 K256 T257 V258 F445 G524 Y525
Binding residue
(residue number reindexed from 1)		G237 G239 K240 T241 V242 F429 G508 Y509
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K256 E279 R280 K456
Catalytic site (residue number reindexed from 1) K240 E263 R264 K440
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0006879 intracellular iron ion homeostasis
GO:0007035 vacuolar acidification
GO:0007042 lysosomal lumen acidification
GO:0015986 proton motive force-driven ATP synthesis
GO:0016241 regulation of macroautophagy
GO:0036295 cellular response to increased oxygen levels
GO:0046034 ATP metabolic process
GO:0048388 endosomal lumen acidification
GO:0051452 intracellular pH reduction
GO:0061795 Golgi lumen acidification
GO:0097401 synaptic vesicle lumen acidification
GO:1902600 proton transmembrane transport
Cellular Component
GO:0000139 Golgi membrane
GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005902 microvillus
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0016469 proton-transporting two-sector ATPase complex
GO:0030133 transport vesicle
GO:0030141 secretory granule
GO:0030665 clathrin-coated vesicle membrane
GO:0031090 organelle membrane
GO:0031410 cytoplasmic vesicle
GO:0033176 proton-transporting V-type ATPase complex
GO:0033180 proton-transporting V-type ATPase, V1 domain
GO:0043231 intracellular membrane-bounded organelle
GO:0070062 extracellular exosome
GO:0098850 extrinsic component of synaptic vesicle membrane
GO:1904949 ATPase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6wm3, PDBe:6wm3, PDBj:6wm3
PDBsum6wm3
PubMed33065002
UniProtP38606|VATA_HUMAN V-type proton ATPase catalytic subunit A (Gene Name=ATP6V1A)

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