Structure of PDB 6vq8 Chain A Binding Site BS01

Receptor Information
>6vq8 Chain A (length=600) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQV
YEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSI
YIPRGVNVSALSRDIKWEFIPSKNLRVGSHITGGDIYGIVNENSLIKHKI
MLPPRSRGSVTYIAPPGNYDASDVVLELEFEGVKEKLSMVQVWPVRQVRP
VTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKY
SNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTS
NMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLA
EMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGD
FSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYD
KHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIK
DDFLQQNGYTPYDRFCPFYKTVGMLSNMISFYDMARRAVETTAQSDNKIT
WSIIREHMGEILYKLSSMKFKDPVKDGEAKIKADYAQLLEDMQNAFRSLE
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 chain6vq8 Chain A 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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PDB6vq8 Structure of V-ATPase from the mammalian brain.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		F252 G253 C254 G255 K256 T257 V258 F445 G524 Y525
Binding residue
(residue number reindexed from 1)		F236 G237 C238 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:0015986 proton motive force-driven ATP synthesis
GO:0036295 cellular response to increased oxygen levels
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:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005902 microvillus
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030133 transport vesicle
GO:0030141 secretory granule
GO:0030665 clathrin-coated vesicle membrane
GO:0033176 proton-transporting V-type ATPase complex
GO:0033180 proton-transporting V-type ATPase, V1 domain
GO:0043231 intracellular membrane-bounded organelle
GO:0098850 extrinsic component of synaptic vesicle membrane
GO:1904949 ATPase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vq8, PDBe:6vq8, PDBj:6vq8
PDBsum6vq8
PubMed32165585
UniProtD4A133

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