Structure of PDB 6xby Chain A Binding Site BS01

Receptor Information
>6xby Chain A (length=597) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQ
VYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQS
IYIPRGVNVSALSRDVKWDFTPCKNLRVGSHITGGDIYGIVNENSLIKHK
IMLPPRNRGTVTYIAPPGNYDTSDVVLELEFEGIKEKFSMVQVWPVRQVR
PVTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSK
YSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANT
SNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRL
AEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGG
DFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYY
DKHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLI
KDDFLQQNGYTPYDRFCPFYKTVGMLSNMIAFYDMARRAVETTAQSDNKI
TWSIIREHMGEILYKLSSMKFKDPVKDGEAKIKADYAQLLEDMQNAF
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 chain6xby Chain D Residue 601 [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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PDB6xby Cryo-EM structures of intact V-ATPase from bovine brain.
Resolution3.79 Å
Binding residue
(original residue number in PDB)		F252 G253 G255 K256 V258 F445 G524 Y525
Binding residue
(residue number reindexed from 1)		F237 G238 G240 K241 V243 F430 G509 Y510
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K256 E279 R280 K456
Catalytic site (residue number reindexed from 1) K241 E264 R265 K441
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
Molecular Function
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:0015986 proton motive force-driven ATP synthesis
GO:0036295 cellular response to increased oxygen levels
GO:0045851 pH reduction
GO:0046034 ATP metabolic process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030133 transport vesicle
GO:0030665 clathrin-coated vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0033180 proton-transporting V-type ATPase, V1 domain

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6xby, PDBe:6xby, PDBj:6xby
PDBsum6xby
PubMed32764564
UniProtP31404|VATA_BOVIN V-type proton ATPase catalytic subunit A (Gene Name=ATP6V1A)

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