Structure of PDB 7nxd Chain A Binding Site BS01

Receptor Information
>7nxd Chain A (length=905) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FNLDAEAPAVLSGPPGSFFGFSVEFYRPGTDGVSVLVGAPKANTSQPGVL
QGGAVYLCPWGASPTQCTPIEFDSKGSRLLESSLSSSEGEEPVEYKSLQW
FGATVRAHGSSILACAPLYSWRTEKEPLSDPVGTCYLSTDNFTRILEYAP
CRSDFSWAAGQGYCQGGFSAEFTKTGRVVLGGPGSYFWQGQILSATQEQI
AESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEFSGDDTEDFVA
GVPKGNLTYGYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLD
DLLVGAPLLMDRTPDGRPQEVGRVYVYLQHPAGIEPTPTLTLTGHDEFGR
FGSSLTPLGDLDQDGYNDVAIGAPFGGETQQGVVFVFPGGPGGLGSKPSQ
VLQPLWAASHTPDFFGSALRGGRDLDGNGYPDLIVGSFGVDKAVVYRGRP
IVSASASLTIFPAMFNPEERSCSLEGNPVACINLSFCLNASGKHVADSIG
FTVELQLDWQKQKGGVRRALFLASRQATLTQTLLIQNGAREDCREMKIYL
RNESEFRDKLSPIHIALNFSLDPQAPVDSHGLRPALHYQSKSRIEDKAQI
LLDCGEDNICVPDLQLEVFGEQNHVYLGDKNALNLTFHAQNVGEGGAYEA
ELRVTAPPEAEYSGLVRHPGNFSSLSCDYFAVNQSRLLVCDLGNPMKAGA
SLWGGLRFTVPHLRDTKKTIQFDFQILSKNLNNSQSDVVSFRLSVEAQAQ
VTLNGVSKPEDLGPAVHHVYELINQGPSSISQGVLELSCPQALEGQQLLY
VTRVTGLNCTTNHPINPKGLEGPQILKCPEAECFRLRCELGPLHQQESQS
LQLHFRVWAKTFLQREHQPFSLQCEAVYKALKMPYRILPRQLPQKERQVA
TAVQW
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain7nxd Chain A Residue 1101 [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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PDB7nxd Structural insights into integrin alpha 5 beta 1 opening by fibronectin ligand.
Resolution4.6 Å
Binding residue
(original residue number in PDB)		E239 S241 D243 T245 D247
Binding residue
(residue number reindexed from 1)		E239 S241 D243 T245 D247
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0005154 epidermal growth factor receptor binding
GO:0005161 platelet-derived growth factor receptor binding
GO:0005178 integrin binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0038023 signaling receptor activity
GO:0043184 vascular endothelial growth factor receptor 2 binding
GO:0046872 metal ion binding
GO:0050839 cell adhesion molecule binding
Biological Process
GO:0001525 angiogenesis
GO:0007044 cell-substrate junction assembly
GO:0007155 cell adhesion
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0007159 leukocyte cell-cell adhesion
GO:0007160 cell-matrix adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0007565 female pregnancy
GO:0007613 memory
GO:0010811 positive regulation of cell-substrate adhesion
GO:0014850 response to muscle activity
GO:0023035 CD40 signaling pathway
GO:0030335 positive regulation of cell migration
GO:0030949 positive regulation of vascular endothelial growth factor receptor signaling pathway
GO:0031589 cell-substrate adhesion
GO:0033627 cell adhesion mediated by integrin
GO:0033631 cell-cell adhesion mediated by integrin
GO:0034113 heterotypic cell-cell adhesion
GO:0035313 wound healing, spreading of epidermal cells
GO:0035987 endodermal cell differentiation
GO:0045765 regulation of angiogenesis
GO:0046718 symbiont entry into host cell
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:0098609 cell-cell adhesion
GO:1903672 positive regulation of sprouting angiogenesis
GO:2000811 negative regulation of anoikis
Cellular Component
GO:0001726 ruffle
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005925 focal adhesion
GO:0008305 integrin complex
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0031410 cytoplasmic vesicle
GO:0032587 ruffle membrane
GO:0034674 integrin alpha5-beta1 complex
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0070161 anchoring junction
GO:0071062 alphav-beta3 integrin-vitronectin complex
GO:0098978 glutamatergic synapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7nxd, PDBe:7nxd, PDBj:7nxd
PDBsum7nxd
PubMed33962943
UniProtP08648|ITA5_HUMAN Integrin alpha-5 (Gene Name=ITGA5)

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