Structure of PDB 8gxx Chain A Binding Site BS01

Receptor Information
>8gxx Chain A (length=578) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIQGVIQKIAGPAVIAKGMLGARMYDICKVGEEGLVGEIIRLDGDTAFVQ
VYEDTSGLKVGEPVVSTGLPLAVELGPGMLNGIYDGIQRPLERIREKTGI
YITRGVVVHALDREKKWAWTPMVKPGDEVRGGMVLGTVPEFGFTHKILVP
PDVRGRVKEVKPAGEYTVEEPVVVLEDGTELKMYHTWPVRRARPVQRKLD
PNTPFLTGMRILDVLFPVAMGGTAAIPGPFGAGKSVTQQSLAKWSNADVV
VYVGCGERGNEMTDVLVEFPELTDPKTGGPLMHRTVLIANTSNMPVAARE
ASIYVGVTIAEYFRDQGFSVALMADSTSRWAEALREISSRLEEMPAEEGY
PPYLAARLAAFYERAGKVITLGGEEGAVTIVGAVSPPGGDMSEPVTQSTL
RIVGAFWRLDASLAFRRHFPAINWNGSYSLFTSALDPWYRENVAEDYPEL
RDAISELLQREAGLQEIVQLVGPDALQDAERLVIEVGRIIREDFLQQNAY
HEVDAYCSMKKAYGIMKMILAFYKEAEAAIKRGVSIDEILQLPVLERIGR
ARYVSEEEFPAYFEEAMKEIQGAFKALA
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 chain8gxx Chain A 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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PDB8gxx Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		G231 A232 G233 K234 S235 V236 F419 A499
Binding residue
(residue number reindexed from 1)		G231 A232 G233 K234 S235 V236 F419 A499
Annotation score5
Enzymatic activity
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:0046933 proton-transporting ATP synthase activity, rotational mechanism
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0006754 ATP biosynthetic process
GO:0042777 proton motive force-driven plasma membrane ATP synthesis
GO:0046034 ATP metabolic process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0045259 proton-transporting ATP synthase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8gxx, PDBe:8gxx, PDBj:8gxx
PDBsum8gxx
PubMed36626983
UniProtQ56403|VATA_THET8 V-type ATP synthase alpha chain (Gene Name=atpA)

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