Structure of PDB 6vqa Chain E Binding Site BS01

Receptor Information
>6vqa Chain E (length=459) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGTKRSGQVLE
VSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKP
IDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQK
IPIFSAAGLPHNEIAAQICRQAGLVKKENFAIVFAAMGVNMETARFFKSD
FEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVIL
TDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRNGS
ITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPS
LSRLMKSAIGEGMTRKDHADVSNQLYACYAIGKDVQAMKAVVGEEALTSD
DLLYLEFLQKFEKNFITQGPYENRTVYETLDIGWQLLRIFPKEMLKRIPQ
STLSEFYPR
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 chain6vqa 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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PDB6vqa Structure of V-ATPase from the mammalian brain.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		R400 K403
Binding residue
(residue number reindexed from 1)		R353 K356
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H199 V236 N237 R400
Catalytic site (residue number reindexed from 1) H161 V189 N190 R353
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0007035 vacuolar acidification
GO:0030641 regulation of cellular pH
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:0005829 cytosol
GO:0005886 plasma membrane
GO:0005902 microvillus
GO:0016324 apical plasma membrane
GO:0030665 clathrin-coated vesicle membrane
GO:0030672 synaptic vesicle 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:0098850 extrinsic component of synaptic vesicle membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vqa, PDBe:6vqa, PDBj:6vqa
PDBsum6vqa
PubMed32165585
UniProtP62815|VATB2_RAT V-type proton ATPase subunit B, brain isoform (Gene Name=Atp6v1b2)

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