Structure of PDB 6rdt Chain T Binding Site BS01

Receptor Information
>6rdt Chain T (length=523) Species: 37502 (Polytomella sp. Pringsheim 198.80) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADAKALDELRKPKFSSKYLIQHVSQKLIPAVKEWEKSYQPPVIHLGRVLS
VGDGIARVYGLKSVQAGELVCFDSGVKGMALNLQADHVGVVVFGNDSVIH
QGDLVYRTGQIVNVPIGPGTLGRVTDGLGQPIDGKGPLTNVRSSLVEVKA
PGIIARQSVREPLFTGVKAVDALVPIGRGQRELIIGDRQTGKTAVAIDAI
IHQKNCNEQVPKAQRVYCVYVAVGQKRSTVAQLVKLFTQTGAMRYTIMVS
ATASDAAPLQFLAPYSGCAMAEYFRDTGKHGLIIYDDLSKQSVAYRQMSL
LLRRPPGREAFPGDVFYLHSRLLERAAKLSKELGGGSLTAFPVIETQAGD
VSAYIATNVISITDGQIFLETELFYKGIRPALNVGLSVSRVGSAAQFPGM
KQVAGTLKLELAQYREVAAFAQFGSDLDAATQYVLERGARLTEMLKQKQF
APIPIERQTVAVYAATKGFLDKVRVQDIVAAEEAVISQVNPAVFKILKAN
GKITPALDAHLKAELRKVKLPGA
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 chain6rdt 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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PDB6rdt Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F 1 -F o coupling.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		R227 Q228 T229 G230 K231 T232 A233 F413 R418 Q486 Q488
Binding residue
(residue number reindexed from 1)		R188 Q189 T190 G191 K192 T193 A194 F374 R379 Q447 Q449
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K231 Q264 K265 R429
Catalytic site (residue number reindexed from 1) K192 Q225 K226 R390
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
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Cellular Component
External links
PDB RCSB:6rdt, PDBe:6rdt, PDBj:6rdt
PDBsum6rdt
PubMed31221832
UniProtA0ZW40

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