Structure of PDB 8t2u Chain B Binding Site BS04

Receptor Information
>8t2u Chain B (length=368) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEARVLEDRPLSDKQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDI
YYLMDLSYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPY
MYISPPEALENPCYDMKTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSR
NRDAPEGGFDAIMQATVCDEKIGWRNDASHLLVFTTDAKTHIALDGRLAG
IVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLSQKNINLIFAVTENV
VNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVRDLPE
ELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSF
TIKPVGFKDSLIVQVTFD
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 chain8t2u Chain B Residue 2003 [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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PDB8t2u Cryo-EM structures of full-length integrin alpha IIb beta 3 in native lipids.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		S123 M124 D126 D127 D251
Binding residue
(residue number reindexed from 1)		S59 M60 D62 D63 D187
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0001968 fibronectin binding
GO:0002020 protease binding
GO:0003756 protein disulfide isomerase activity
GO:0005080 protein kinase C binding
GO:0005161 platelet-derived growth factor receptor binding
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0015026 coreceptor activity
GO:0017134 fibroblast growth factor binding
GO:0019899 enzyme binding
GO:0019960 C-X3-C chemokine binding
GO:0031994 insulin-like growth factor I binding
GO:0038132 neuregulin binding
GO:0042802 identical protein binding
GO:0043184 vascular endothelial growth factor receptor 2 binding
GO:0046872 metal ion binding
GO:0050839 cell adhesion molecule binding
GO:0050840 extracellular matrix binding
GO:0070051 fibrinogen binding
Biological Process
GO:0001934 positive regulation of protein phosphorylation
GO:0001938 positive regulation of endothelial cell proliferation
GO:0001954 positive regulation of cell-matrix adhesion
GO:0002687 positive regulation of leukocyte migration
GO:0007044 cell-substrate junction assembly
GO:0007155 cell adhesion
GO:0007160 cell-matrix adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0007566 embryo implantation
GO:0007596 blood coagulation
GO:0008277 regulation of G protein-coupled receptor signaling pathway
GO:0010595 positive regulation of endothelial cell migration
GO:0010628 positive regulation of gene expression
GO:0010745 negative regulation of macrophage derived foam cell differentiation
GO:0010763 positive regulation of fibroblast migration
GO:0010888 negative regulation of lipid storage
GO:0014823 response to activity
GO:0014909 smooth muscle cell migration
GO:0014911 positive regulation of smooth muscle cell migration
GO:0030168 platelet activation
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:0032147 activation of protein kinase activity
GO:0032369 negative regulation of lipid transport
GO:0032880 regulation of protein localization
GO:0032956 regulation of actin cytoskeleton organization
GO:0033627 cell adhesion mediated by integrin
GO:0033630 positive regulation of cell adhesion mediated by integrin
GO:0033690 positive regulation of osteoblast proliferation
GO:0034113 heterotypic cell-cell adhesion
GO:0034446 substrate adhesion-dependent cell spreading
GO:0035295 tube development
GO:0035313 wound healing, spreading of epidermal cells
GO:0036119 response to platelet-derived growth factor
GO:0036120 cellular response to platelet-derived growth factor stimulus
GO:0038027 apolipoprotein A-I-mediated signaling pathway
GO:0042060 wound healing
GO:0043277 apoptotic cell clearance
GO:0045124 regulation of bone resorption
GO:0045766 positive regulation of angiogenesis
GO:0045780 positive regulation of bone resorption
GO:0046718 symbiont entry into host cell
GO:0048008 platelet-derived growth factor receptor signaling pathway
GO:0048146 positive regulation of fibroblast proliferation
GO:0048333 mesodermal cell differentiation
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:0050748 negative regulation of lipoprotein metabolic process
GO:0050919 negative chemotaxis
GO:0051279 regulation of release of sequestered calcium ion into cytosol
GO:0051611 regulation of serotonin uptake
GO:0060055 angiogenesis involved in wound healing
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0070527 platelet aggregation
GO:0071260 cellular response to mechanical stimulus
GO:0071466 cellular response to xenobiotic stimulus
GO:0072126 positive regulation of glomerular mesangial cell proliferation
GO:0072378 blood coagulation, fibrin clot formation
GO:0098880 maintenance of postsynaptic specialization structure
GO:0099149 regulation of postsynaptic neurotransmitter receptor internalization
GO:0150054 regulation of postsynaptic neurotransmitter receptor diffusion trapping
GO:1900026 positive regulation of substrate adhesion-dependent cell spreading
GO:1900731 positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway
GO:1901163 regulation of trophoblast cell migration
GO:1903053 regulation of extracellular matrix organization
GO:1905598 negative regulation of low-density lipoprotein receptor activity
GO:1990314 cellular response to insulin-like growth factor stimulus
GO:2000352 negative regulation of endothelial cell apoptotic process
GO:2000406 positive regulation of T cell migration
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
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:0016324 apical plasma membrane
GO:0031092 platelet alpha granule membrane
GO:0031258 lamellipodium membrane
GO:0031527 filopodium membrane
GO:0031528 microvillus membrane
GO:0032587 ruffle membrane
GO:0032991 protein-containing complex
GO:0034683 integrin alphav-beta3 complex
GO:0035866 alphav-beta3 integrin-PKCalpha complex
GO:0035867 alphav-beta3 integrin-IGF-1-IGF1R complex
GO:0035868 alphav-beta3 integrin-HMGB1 complex
GO:0042470 melanosome
GO:0042995 cell projection
GO:0043235 receptor complex
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0070062 extracellular exosome
GO:0070161 anchoring junction
GO:0070442 integrin alphaIIb-beta3 complex
GO:0071062 alphav-beta3 integrin-vitronectin complex
GO:0071133 alpha9-beta1 integrin-ADAM8 complex
GO:0097060 synaptic membrane
GO:0098690 glycinergic synapse
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8t2u, PDBe:8t2u, PDBj:8t2u
PDBsum8t2u
PubMed37443315
UniProtP05106|ITB3_HUMAN Integrin beta-3 (Gene Name=ITGB3)

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