Structure of PDB 6rdh Chain Y Binding Site BS01

Receptor Information
>6rdh Chain Y (length=521) Species: 37502 (Polytomella sp. Pringsheim 198.80) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DAGYVSQVIGPVVDVRFDGELPSILSSLEVEGHSVRLVLEVAQHMGDNTV
RCIAMDSTDGLVRGQKVVDTGSPIKVPVGRGTLGRIMNVIGEPVDEQGPI
DAADIWSIHREAPEFTEQSTEQEILVTGIKVVDLLAPYQRGGKIGLFGGA
GVGKTVLIMELINNVAKAHGGFSVFAGVGERTREGNDLYREMIESGVIKL
GAERGNSKCTLVYGQMNEPPGARARVALTGLTVAEYFRDIEGQDVLLFVD
NIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGGLQERITTTTKGSITS
VQAVYVPADDLTDPAPATTFAHLDATTVLSRSIAELGIYPAVDPLDSTSR
MLNPNVIGAEHYNVARGVQKVLQDYKNLQDIIAILGMDELSEEDKLTVAR
ARKIQRFLSQPFQVAEVFTGTPGKYVDLADTISGFQGVLTGKYDDLPEMA
FYMVGDIKEVKEKADKMAKDIASRKEADNKKVSEELKDIPSLDKLVSEIK
EVVIEEDDGLEEDFKAEALSS
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 chain6rdh Chain Y 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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PDB6rdh Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F 1 -F o coupling.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		G186 G188 K189 T190 V191 Y374 F447 F453
Binding residue
(residue number reindexed from 1)		G151 G153 K154 T155 V156 Y339 F412 F418
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K189 E215 R216 R385
Catalytic site (residue number reindexed from 1) K154 E180 R181 R350
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016787 hydrolase activity
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:0016020 membrane
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:6rdh, PDBe:6rdh, PDBj:6rdh
PDBsum6rdh
PubMed31221832
UniProtA0ZW41

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