Structure of PDB 6rdk Chain X Binding Site BS01

Receptor Information
>6rdk Chain X (length=542) Species: 37502 (Polytomella sp. Pringsheim 198.80) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAIDAGYVSQVIGPVVDVRFDGELPSILSSLEVEGHSVRLVLEVAQHMGD
NTVRCIAMDSTDGLVRGQKVVDTGSPIKVPVGRGTLGRIMNVIGEPVDEQ
GPIDAADIWSIHREAPEFTEQSTEQEILVTGIKVVDLLAPYQRGGKIGLF
GGAGVGKTVLIMELINNVAKAHGGFSVFAGVGERTREGNDLYREMIESGV
IKLGAERGNSKCTLVYGQMNEPPGARARVALTGLTVAEYFRDIEGQDVLL
FVDNIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGGLQERITTTTKGS
ITSVQAVYVPADDLTDPAPATTFAHLDATTVLSRSIAELGIYPAVDPLDS
TSRMLNPNVIGAEHYNVARGVQKVLQDYKNLQDIIAILGMDELSEEDKLT
VARARKIQRFLSQPFQVAEVFTGTPGKYVDLADTISGFQGVLTGKYDDLP
EMAFYMVGDIKEVKEKADKMAKDIASRKEADNKKVSEELKDIPSLDKLVS
EIKEVVIEEDDGLEEDFKAEALSSETVVLNEEGKSVPLPKKN
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 chain6rdk Chain T Residue 1001 [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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PDB6rdk Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F 1 -F o coupling.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		R385 N388
Binding residue
(residue number reindexed from 1)		R353 N356
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K189 E215 R216 R385
Catalytic site (residue number reindexed from 1) K157 E183 R184 R353
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
View graph for
Cellular Component
External links
PDB RCSB:6rdk, PDBe:6rdk, PDBj:6rdk
PDBsum6rdk
PubMed31221832
UniProtA0ZW41

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