Structure of PDB 8h9l Chain F Binding Site BS01

Receptor Information

>8h9l Chain F (length=466) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ATGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTV
RTIAMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIGEPIDERGPI
KTKQFAPIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGA
GVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINL
KDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNI
FRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQ
AIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIM
DPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRAR
KIQRFLSQPFQVAEVFTGHMGKLVPLKETIKGFQQILAGEYDHLPEQAFY
MVGPIEEAVAKADKLA

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

8h9l Chain F 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	8h9l Structure of the human ATP synthase.
Resolution	2.61 Å
Binding residue (original residue number in PDB)	G162 G164 K165 T166 V167 Y348 F421 F427
Binding residue (residue number reindexed from 1)	G151 G153 K154 T155 V156 Y337 F410 F416
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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Cellular Component

External links

PDB	RCSB:8h9l, PDBe:8h9l, PDBj:8h9l
PDBsum	8h9l
PubMed	37244256
UniProt	P06576\|ATPB_HUMAN ATP synthase subunit beta, mitochondrial (Gene Name=ATP5F1B)

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