Structure of PDB 7nxd Chain B Binding Site BS03

Receptor Information
>7nxd Chain B (length=690) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPTSARCDDLEALKK
KGCPPDDIENPRGSKDIKKNKNVTNRSKGTAEKLKPEDIHQIQPQQLVLR
LRSGEPQTFTLKFKRAEDYPIDLYYLMDLSYSMKDDLENVKSLGTDLMNE
MRRITSDFRIGFGSFVEKTVMPYISTTPAKLRNPCTSEQNCTTPFSYKNV
LSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAVCGSLIGWRNVTR
LLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIAHL
VQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLII
DAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGD
EVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYICECECQSEGIP
ESPKCHEGNGTFECGACRCNEGRVGRHCECSTDEVNSEDMDAYCRKENSS
EICSNNGECVCGQCVCRKRDNTNEIYSGKFCECDNFNCDRSNGLICGGNG
VCKCRVCECNPNYTGSACDCSLDTSTCEASNGQICNGRGICECGVCKCTD
PKFQGQTCEMCQTCLGVCAEHKECVQCRAFNKGEKCTQECSYFNITKVES
RDKLVSHCKEKDVDDCWFYFTYSVNGNNEVMVHVVENPEC
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 B Residue 1003 [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)		E169 N224 D226 P228 E229
Binding residue
(residue number reindexed from 1)		E167 N222 D224 P226 E227
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0001618 virus receptor activity
GO:0001968 fibronectin binding
GO:0002020 protease binding
GO:0003779 actin binding
GO:0005178 integrin binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0015026 coreceptor activity
GO:0019901 protein kinase binding
GO:0019960 C-X3-C chemokine binding
GO:0038023 signaling receptor activity
GO:0043236 laminin binding
GO:0044877 protein-containing complex binding
GO:0045296 cadherin binding
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity
GO:0050839 cell adhesion molecule binding
GO:0098639 collagen binding involved in cell-matrix adhesion
GO:0098640 integrin binding involved in cell-matrix adhesion
GO:1990782 protein tyrosine kinase binding
Biological Process
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000132 establishment of mitotic spindle orientation
GO:0001525 angiogenesis
GO:0001701 in utero embryonic development
GO:0002042 cell migration involved in sprouting angiogenesis
GO:0002052 positive regulation of neuroblast proliferation
GO:0006909 phagocytosis
GO:0006968 cellular defense response
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007159 leukocyte cell-cell adhesion
GO:0007160 cell-matrix adhesion
GO:0007161 calcium-independent cell-matrix adhesion
GO:0007179 transforming growth factor beta receptor signaling pathway
GO:0007229 integrin-mediated signaling pathway
GO:0007405 neuroblast proliferation
GO:0007517 muscle organ development
GO:0007520 myoblast fusion
GO:0008283 cell population proliferation
GO:0008354 germ cell migration
GO:0008542 visual learning
GO:0010710 regulation of collagen catabolic process
GO:0010763 positive regulation of fibroblast migration
GO:0014850 response to muscle activity
GO:0016477 cell migration
GO:0021943 formation of radial glial scaffolds
GO:0023035 CD40 signaling pathway
GO:0030030 cell projection organization
GO:0030032 lamellipodium assembly
GO:0030182 neuron differentiation
GO:0030183 B cell differentiation
GO:0030198 extracellular matrix organization
GO:0030335 positive regulation of cell migration
GO:0031175 neuron projection development
GO:0031589 cell-substrate adhesion
GO:0031623 receptor internalization
GO:0033627 cell adhesion mediated by integrin
GO:0033631 cell-cell adhesion mediated by integrin
GO:0034113 heterotypic cell-cell adhesion
GO:0035024 negative regulation of Rho protein signal transduction
GO:0035313 wound healing, spreading of epidermal cells
GO:0035633 maintenance of blood-brain barrier
GO:0043065 positive regulation of apoptotic process
GO:0043149 stress fiber assembly
GO:0043547 positive regulation of GTPase activity
GO:0045214 sarcomere organization
GO:0045445 myoblast differentiation
GO:0045665 negative regulation of neuron differentiation
GO:0045743 positive regulation of fibroblast growth factor receptor signaling pathway
GO:0045766 positive regulation of angiogenesis
GO:0045906 negative regulation of vasoconstriction
GO:0046718 symbiont entry into host cell
GO:0048333 mesodermal cell differentiation
GO:0048626 myoblast fate specification
GO:0048675 axon extension
GO:0048813 dendrite morphogenesis
GO:0050804 modulation of chemical synaptic transmission
GO:0050901 leukocyte tethering or rolling
GO:0051726 regulation of cell cycle
GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0051951 positive regulation of glutamate uptake involved in transmission of nerve impulse
GO:0055007 cardiac muscle cell differentiation
GO:0060379 cardiac muscle cell myoblast differentiation
GO:0060912 cardiac cell fate specification
GO:0071404 cellular response to low-density lipoprotein particle stimulus
GO:0071711 basement membrane organization
GO:0090303 positive regulation of wound healing
GO:0098609 cell-cell adhesion
GO:0150003 regulation of spontaneous synaptic transmission
GO:0150103 reactive gliosis
GO:1900748 positive regulation of vascular endothelial growth factor signaling pathway
GO:1901979 regulation of inward rectifier potassium channel activity
GO:1903078 positive regulation of protein localization to plasma membrane
GO:1905806 regulation of synapse pruning
GO:2000811 negative regulation of anoikis
Cellular Component
GO:0001726 ruffle
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0008305 integrin complex
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0010008 endosome membrane
GO:0014704 intercalated disc
GO:0016020 membrane
GO:0030027 lamellipodium
GO:0030175 filopodium
GO:0031410 cytoplasmic vesicle
GO:0031594 neuromuscular junction
GO:0032154 cleavage furrow
GO:0032587 ruffle membrane
GO:0034665 integrin alpha1-beta1 complex
GO:0034666 integrin alpha2-beta1 complex
GO:0034667 integrin alpha3-beta1 complex
GO:0034668 integrin alpha4-beta1 complex
GO:0034674 integrin alpha5-beta1 complex
GO:0034675 integrin alpha6-beta1 complex
GO:0034677 integrin alpha7-beta1 complex
GO:0034678 integrin alpha8-beta1 complex
GO:0034679 integrin alpha9-beta1 complex
GO:0034680 integrin alpha10-beta1 complex
GO:0034681 integrin alpha11-beta1 complex
GO:0034682 integrin alphav-beta1 complex
GO:0035748 myelin sheath abaxonal region
GO:0042383 sarcolemma
GO:0042470 melanosome
GO:0042995 cell projection
GO:0043197 dendritic spine
GO:0043235 receptor complex
GO:0045121 membrane raft
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0055037 recycling endosome
GO:0070062 extracellular exosome
GO:0070161 anchoring junction
GO:0097060 synaptic membrane
GO:0097386 glial cell projection
GO:0098685 Schaffer collateral - CA1 synapse
GO:0098978 glutamatergic synapse
GO:0150053 cerebellar climbing fiber to Purkinje cell synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7nxd, PDBe:7nxd, PDBj:7nxd
PDBsum7nxd
PubMed33962943
UniProtP05556|ITB1_HUMAN Integrin beta-1 (Gene Name=ITGB1)

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