Structure of PDB 8dbp Chain D Binding Site BS01

Receptor Information
>8dbp Chain D (length=460) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MATGKIVQVIGAVVDVEFPQDAVPRVYDALEVQNGNERLVLEVQQQLGGG
IVRTIAMGSSDGLRRGLDVKDLEHPIEVPVGKATLGRIMNVLGEPVDMKG
EIGEEERWAIHRAAPSYEELSNSQELLETGIKVIDLMAPFAKGGKVGLFG
GAGVGKTVNMMELIRNIAIEHSGYSVFAGVGERTREGNDFYHEMTDSNVI
DKVSLVYGQMNEPPGNRLRVALTGLTMAEKFRDEGRDVLLFVDNIYRYTL
AGTEVSALLGRMPSAVGYQPTLAEEMGVLQERITSTKTGSITSVQAVYVP
ADDLTDPSPATTFAHLDATVVLSRQIASLGIYPAVDPLDSTSRQLDPLVV
GQEHYDTARGVQSILQRYQELKDIIAILGMDELSEEDKLVVARARKIQRF
LSQPFFVAEVFTGSPGKYVSLKDTIRGFKGIMEGEYDHLPEQAFYMVGSI
EEAVEKAKKL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8dbp Chain B 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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PDB8dbp Changes within the central stalk of E. coli F 1 F o ATP synthase observed after addition of ATP.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		R342 D345
Binding residue
(residue number reindexed from 1)		R343 D346
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:0016887 ATP hydrolysis activity
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:0015986 proton motive force-driven ATP synthesis
GO:0042777 proton motive force-driven plasma membrane ATP synthesis
GO:0046034 ATP metabolic process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0045259 proton-transporting ATP synthase complex
GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1)

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dbp, PDBe:8dbp, PDBj:8dbp
PDBsum8dbp
PubMed36631659
UniProtP0ABB4|ATPB_ECOLI ATP synthase subunit beta (Gene Name=atpD)

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