Structure of PDB 5y5y Chain C Binding Site BS01

Receptor Information
>5y5y Chain C (length=577) 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
PNTPFLTGMRILDVLFPVAMGGTAAIPGPFGSGKTVTQQSLAKWSNADVV
VYVGCGERGNEMTDVLVEFPELTDPKTGGPLMHRTVLIANTSNMPVAARE
ASIYVGVTIAEYFRDQGFSVALMADSTSRWAEALREISSRLEEMPAEEGY
PPYLAARLAAFYERAGKVITLGGEEGAVTIVGAVSPPGGDMSEPVTQSTL
RIVGAFWRLDASLAFRRHFPAINWNGSYSLFTSALDPWYRENVAEDYPEL
RDAISELLQREAGLQEIVQLVGPDALQDAERLVIEVGRIIREDFLQQNAY
HEVDAYCSMKKAYGIMKMILAFYKEAEAAIKRGVSIDEILQLPVLERIGR
ARYVSEEEFPAYFEEAMKEIQGAFKAL
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 chain5y5y Chain C Residue 600 [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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PDB5y5y Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus
Resolution4.7 Å
Binding residue
(original residue number in PDB)		G231 S232 G233 K234 T235 V236 R417 H418 F419
Binding residue
(residue number reindexed from 1)		G231 S232 G233 K234 T235 V236 R417 H418 F419
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K234 E257 R258 L430
Catalytic site (residue number reindexed from 1) K234 E257 R258 L430
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:5y5y, PDBe:5y5y, PDBj:5y5y
PDBsum5y5y
PubMed29311594
UniProtQ56403|VATA_THET8 V-type ATP synthase alpha chain (Gene Name=atpA)

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