Structure of PDB 6rdl Chain V Binding Site BS01

Receptor Information
>6rdl Chain V (length=520) Species: 37502 (Polytomella sp. Pringsheim 198.80) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KALDELRKPKFSSKYLIQHVSQKLIPAVKEWEKSYQPPVIHLGRVLSVGD
GIARVYGLKSVQAGELVCFDSGVKGMALNLQADHVGVVVFGNDSVIHQGD
LVYRTGQIVNVPIGPGTLGRVTDGLGQPIDGKGPLTNVRSSLVEVKAPGI
IARQSVREPLFTGVKAVDALVPIGRGQRELIIGDRQTGKTAVAIDAIIHQ
KNCNEQVPKAQRVYCVYVAVGQKRSTVAQLVKLFTQTGAMRYTIMVSATA
SDAAPLQFLAPYSGCAMAEYFRDTGKHGLIIYDDLSKQSVAYRQMSLLLR
RPPGREAFPGDVFYLHSRLLERAAKLSKELGGGSLTAFPVIETQAGDVSA
YIATNVISITDGQIFLETELFYKGIRPALNVGLSVSRVGSAAQFPGMKQV
AGTLKLELAQYREVAAFAQFGSDLDAATQYVLERGARLTEMLKQKQFAPI
PIERQTVAVYAATKGFLDKVRVQDIVAAEEAVISQVNPAVFKILKANGKI
TPALDAHLKAELRKVKLPGA
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 chain6rdl Chain V 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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PDB6rdl 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)		Q228 G230 K231 T232 A233 F413 R418 Q486 Q488
Binding residue
(residue number reindexed from 1)		Q186 G188 K189 T190 A191 F371 R376 Q444 Q446
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K231 Q264 K265 R429
Catalytic site (residue number reindexed from 1) K189 Q222 K223 R387
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0032559 adenyl ribonucleotide binding
GO:0043531 ADP binding
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
Biological Process
GO:0006754 ATP biosynthetic process
GO:0015986 proton motive force-driven ATP synthesis
GO:0046034 ATP metabolic process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner 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:6rdl, PDBe:6rdl, PDBj:6rdl
PDBsum6rdl
PubMed31221832
UniProtA0ZW40

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