Structure of PDB 6vmb Chain D Binding Site BS02

Receptor Information
>6vmb Chain D (length=478) Species: 3562 (Spinacia oleracea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKNLGRIAQIIGPVLDVAFPPGKMPNIYNALIVKGRDTAGQPMNVTCEVQ
QLLGNNRVRAVAMSATDGLTRGMEVIDTGAPLSVPVGGATLGRIFNVLGE
PVDNLGPVDTRTTSPIHRSAPAFTQLDTKLSIFETGIKVVDLLAPYRRGG
KIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVGERTREGNDLYMEM
KESGVINEQNIAESKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQ
DVLLFIDNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERITST
KEGSITSIQAVYVPADDLTDPAPATTFAHLDATTVLSRGLAAKGIYPAVD
PLDSTSTMLQPRIVGEEHYEIAQRVKETLQRYKELQDIIAILGLDELSEE
DRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGLAETIRGFQLILSGEL
DSLPEQAFYLVGNIDEATAKAMNLEMES
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 chain6vmb Chain D Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vmb Structural basis of redox modulation on chloroplast ATP synthase.
Resolution5.23 Å
Binding residue
(original residue number in PDB)		G175 V176 G177 K178 T179 V180 R205 Y362 F441
Binding residue
(residue number reindexed from 1)		G159 V160 G161 K162 T163 V164 R189 Y346 F425
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K178 E204 R205 T373
Catalytic site (residue number reindexed from 1) K162 E188 R189 T357
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
Molecular Function
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:0042776 proton motive force-driven mitochondrial ATP synthesis
GO:0046034 ATP metabolic process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0009507 chloroplast
GO:0009535 chloroplast thylakoid membrane
GO:0009579 thylakoid
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
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Cellular Component
External links
PDB RCSB:6vmb, PDBe:6vmb, PDBj:6vmb
PDBsum6vmb
PubMed32879423
UniProtP00825|ATPB_SPIOL ATP synthase subunit beta, chloroplastic (Gene Name=atpB)

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