Structure of PDB 8h9e Chain D Binding Site BS01

Receptor Information

>8h9e 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 ID

ADP

InChI

InChI=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

InChIKey

XTWYTFMLZFPYCI-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(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 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H15 N5 O10 P2

Name

ADENOSINE-5'-DIPHOSPHATE

PDB chain

8h9e 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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Structure summary

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PDB	8h9e Structure of the human ATP synthase.
Resolution	2.53 Å
Binding residue (original residue number in PDB)	G162 G164 K165 T166 V167 Y348
Binding residue (residue number reindexed from 1)	G152 G154 K155 T156 V157 Y338
Annotation score	5

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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Cellular Component

External links

PDB	RCSB:8h9e, PDBe:8h9e, PDBj:8h9e
PDBsum	8h9e
PubMed	37244256
UniProt	P06576\|ATPB_HUMAN ATP synthase subunit beta, mitochondrial (Gene Name=ATP5F1B)

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