Structure of PDB 6vmd Chain E Binding Site BS01

Receptor Information
>6vmd Chain E (length=481) Species: 3562 (Spinacia oleracea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKKNLGRIAQIIGPVLDVAFPPGKMPNIYNALIVKGRDTAGQPMNVTCEV
QQLLGNNRVRAVAMSATDGLTRGMEVIDTGAPLSVPVGGATLGRIFNVLG
EPVDNLGPVDTRTTSPIHRSAPAFTQLDTKLSIFETGIKVVDLLAPYRRG
GKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVGERTREGNDLYME
MKESGVINEQNIAESKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNE
QDVLLFIDNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERITS
TKEGSITSIQAVYVPADDLTDPAPATTFAHLDATTVLSRGLAAKGIYPAV
DPLDSTSTMLQPRIVGEEHYEIAQRVKETLQRYKELQDIIAILGLDELSE
EDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGLAETIRGFQLILSGE
LDSLPEQAFYLVGNIDEATAKAMNLEMESKL
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 chain6vmd 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6vmd Structural basis of redox modulation on chloroplast ATP synthase.
Resolution4.53 Å
Binding residue
(original residue number in PDB)		Q376 R378
Binding residue
(residue number reindexed from 1)		Q361 R363
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K178 E204 R205 T373
Catalytic site (residue number reindexed from 1) K163 E189 R190 T358
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)

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6vmd, PDBe:6vmd, PDBj:6vmd
PDBsum6vmd
PubMed32879423
UniProtP00825|ATPB_SPIOL ATP synthase subunit beta, chloroplastic (Gene Name=atpB)

[Back to BioLiP]