Structure of PDB 8f29 Chain D Binding Site BS01

Receptor Information
>8f29 Chain D (length=473) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STPITGKVTAVIGAIVDVHFEQSELPAILNALEIKTPQGKLVLEVAQHLG
ENTVRTIAMDGTEGLVRGEKVLDTGGPISVPVGRETLGRIINVIGEPIDE
RGPIKSKLRKPIHADPPSFAEQSTSAEILETGIKVVDLLAPYARGGKIGL
FGGAGVGKTVFIQELINNIAKAHGGFSVFTGVGERTREGNDLYREMKETG
VINLEGESKVALVFGQMNEPPGARARVALTGLTIAEYFRDEEGQDVLLFI
DNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGLLQERITTTKKGSVT
SVQAVYVPADDLTDPAPATTFAHLDATTVLSRGISELGIYPAVDPLDSKS
RLLDAAVVGQEHYDVASKVQETLQTYKSLQDIIAILGMDELSEQDKLTVE
RARKIQRFLSQPFAVAEVFTGIPGKLVRLKDTVASFKAVLEGKYDNIPEH
AFYMVGGIEDVVAKAEKLAAEAN
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 chain8f29 Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8f29 Yeast ATP synthase in conformation-1 at pH 6
Resolution4.0 Å
Binding residue
(original residue number in PDB)		A159 G160 V161 G162 K163 T164 V165 E193 Y345 F418 A421 F424
Binding residue
(residue number reindexed from 1)		A154 G155 V156 G157 K158 T159 V160 E188 Y340 F413 A416 F419
Annotation score5
Enzymatic activity
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
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:0005743 mitochondrial inner membrane
GO:0005758 mitochondrial intermembrane space
GO:0005829 cytosol
GO:0016020 membrane
GO:0045259 proton-transporting ATP synthase complex
GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1)
GO:0045267 proton-transporting ATP synthase, catalytic core

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8f29, PDBe:8f29, PDBj:8f29
PDBsum8f29
PubMed38316880
UniProtP00830|ATPB_YEAST ATP synthase subunit beta, mitochondrial (Gene Name=ATP2)

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