Structure of PDB 8ki3 Chain D Binding Site BS01

Receptor Information
>8ki3 Chain D (length=470) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AATGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGEST
VRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIGEPIDERGP
IKTKQFAPIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGG
AGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVIN
LKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDN
IFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSV
QAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRI
MDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRA
RKIQRFLSQPFQVAEVFTGHMGKLVPLKETIKGFQQILAGEYDHLPEQAF
YMVGPIEEAVAKADKLAEEH
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 chain8ki3 Chain D Residue 501 [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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PDB8ki3 Structure of Mycobacterium tuberculosis ATP synthase
Resolution2.89 Å
Binding residue
(original residue number in PDB)		G162 G164 K165 T166 V167 Y348 F421 A424
Binding residue
(residue number reindexed from 1)		G152 G154 K155 T156 V157 Y338 F411 A414
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:0042288 MHC class I protein binding
GO:0043532 angiostatin binding
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0001525 angiogenesis
GO:0001649 osteoblast differentiation
GO:0006091 generation of precursor metabolites and energy
GO:0006629 lipid metabolic process
GO:0006754 ATP biosynthetic process
GO:0006933 negative regulation of cell adhesion involved in substrate-bound cell migration
GO:0015986 proton motive force-driven ATP synthesis
GO:0042776 proton motive force-driven mitochondrial ATP synthesis
GO:0043536 positive regulation of blood vessel endothelial cell migration
GO:0046034 ATP metabolic process
GO:0051453 regulation of intracellular pH
GO:0098761 cellular response to interleukin-7
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016469 proton-transporting two-sector ATPase complex
GO:0031090 organelle membrane
GO:0031966 mitochondrial membrane
GO:0042645 mitochondrial nucleoid
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
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ki3, PDBe:8ki3, PDBj:8ki3
PDBsum8ki3
PubMed38961288
UniProtP06576|ATPB_HUMAN ATP synthase subunit beta, mitochondrial (Gene Name=ATP5F1B)

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