5E6V

Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e5e6vA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF17205	e5e6vA2	A: few secondary structure elements	X: Trefoil/Plexin domain-like (From Topology)	H: Trefoil/Plexin domain-like (From Topology)	T: Trefoil/Plexin domain-like	F: PF17205	ECOD (1.6)
A	PF18372	e5e6vA3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: PF18372	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00362	Integrin beta chain VWA domain (Integrin_beta)	Integrin beta chain VWA domain	Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer [1]. This domain corresponds to the integrin beta VWA domain.	Domain
A	PF17205	Integrin plexin domain (PSI_integrin)	Integrin plexin domain	This short disulphide rich domain is found at the N-terminus of integrin beta chains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Integrin beta-2	amide binding amyloid-beta binding binding peptide binding protein binding heat shock protein binding opsonin binding complement component C3b binding complement binding cation binding ion binding metal ion binding small molecule binding cell adhesion molecule binding amide binding amyloid-beta binding binding peptide binding protein binding heat shock protein binding opsonin binding complement component C3b binding complement binding cation binding ion binding metal ion binding small molecule binding cell adhesion molecule binding ICAM-3 receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein-containing complex binding integrin binding signaling receptor binding kinase binding enzyme binding protein kinase binding	regulation of biological process regulation of cellular process cellular metabolic process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process regulation of cellular metabolic process positive regulation of cellular metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process regulation of biological process regulation of cellular process cellular metabolic process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process regulation of cellular metabolic process positive regulation of cellular metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process cellular process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of metabolic process regulation of reactive oxygen species metabolic process positive regulation of cellular process membrane organization import into cell transport establishment of localization vesicle-mediated transport cellular component organization localization phagocytosis, engulfment membrane invagination phagocytosis cellular component organization or biogenesis endocytosis plasma membrane invagination receptor internalization receptor-mediated endocytosis regulation of protein modification process regulation of protein phosphorylation peptidyl-tyrosine modification regulation of primary metabolic process organic substance metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process organonitrogen compound metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation primary metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation cell chemotaxis cellular response to stimulus chemotaxis response to stimulus neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion apoptotic process cell death programmed cell death signaling cell-cell signaling cell communication response to organic substance response to endogenous stimulus response to organonitrogen compound response to lipoprotein particle response to nitrogen compound cellular response to low-density lipoprotein particle stimulus cellular response to lipoprotein particle stimulus cell adhesion organic hydroxy compound metabolic process negative regulation of biological process dopamine metabolic process catechol-containing compound metabolic process catecholamine metabolic process regulation of dopamine metabolic process negative regulation of dopamine metabolic process regulation of amine metabolic process negative regulation of metabolic process negative regulation of catecholamine metabolic process organic cyclic compound metabolic process amine metabolic process phenol-containing compound metabolic process negative regulation of amine metabolic process regulation of catecholamine metabolic process biogenic amine metabolic process cell-cell adhesion leukocyte cell-cell adhesion heterotypic cell-cell adhesion regulation of immune effector process neutrophil activation multicellular organismal process regulation of localization regulation of myeloid leukocyte mediated immunity positive regulation of leukocyte mediated immunity regulated exocytosis cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity myeloid leukocyte activation neutrophil activation involved in immune response positive regulation of leukocyte degranulation positive regulation of immune response positive regulation of regulated secretory pathway establishment of localization in cell leukocyte mediated immunity regulation of immune system process positive regulation of immune system process immune response immune effector process regulation of secretion regulation of leukocyte mediated immunity exocytosis regulation of response to stimulus positive regulation of myeloid leukocyte mediated immunity regulation of immune response cellular localization positive regulation of secretion by cell positive regulation of exocytosis leukocyte activation positive regulation of response to stimulus regulation of regulated secretory pathway neutrophil mediated immunity secretion by cell regulation of secretion by cell positive regulation of secretion regulation of neutrophil degranulation leukocyte activation involved in immune response neutrophil degranulation positive regulation of immune effector process regulation of leukocyte degranulation secretion regulation of transport cell activation export from cell regulation of vesicle-mediated transport myeloid cell activation involved in immune response positive regulation of transport regulation of exocytosis positive regulation of neutrophil degranulation granulocyte activation protein localization receptor clustering cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane defense response macrophage activation response to stress leukocyte activation involved in inflammatory response microglial cell activation inflammatory response glial cell activation neuroinflammatory response establishment of protein localization regulation of protein localization protein targeting positive regulation of establishment of protein localization regulation of protein targeting to membrane regulation of protein localization to membrane establishment of protein localization to membrane regulation of establishment of protein localization positive regulation of protein localization to membrane protein targeting to membrane regulation of cellular localization regulation of protein targeting positive regulation of protein localization positive regulation of protein targeting to membrane cell-cell adhesion via plasma-membrane adhesion molecules cell-matrix adhesion cell-substrate adhesion developmental process formation of primary germ layer cellular developmental process embryonic morphogenesis tissue development embryo development gastrulation anatomical structure morphogenesis multicellular organism development endoderm development cell differentiation anatomical structure development anatomical structure formation involved in morphogenesis endoderm formation endodermal cell differentiation amyloid-beta clearance integrin-mediated signaling pathway cell surface receptor signaling pathway signal transduction regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis regulation of isomerase activity regulation of molecular function positive regulation of molecular function positive regulation of prostaglandin-E synthase activity regulation of catalytic activity positive regulation of catalytic activity positive regulation of isomerase activity regulation of prostaglandin-E synthase activity positive regulation of cell adhesion regulation of cell adhesion positive regulation of leukocyte cell-cell adhesion positive regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte adhesion to vascular endothelial cell positive regulation of cell-cell adhesion leukocyte adhesion to vascular endothelial cell regulation of leukocyte cell-cell adhesion regulation of cell-cell adhesion	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule cell periphery cell surface plasma membrane external side of plasma membrane side of membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle protein-containing complex receptor complex tertiary granule membrane tertiary granule anchoring junction cell junction focal adhesion cell-substrate junction plasma membrane protein complex membrane protein complex integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion integrin alphaL-beta2 complex integrin alphaX-beta2 complex integrin alphaM-beta2 complex ficolin-1-rich granule membrane ficolin-1-rich granule membrane microdomain membrane raft plasma membrane raft plasma membrane region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR033760	Integrin beta N-terminal	Domain
A	IPR036349	Integrin beta tail domain superfamily	Homologous Superfamily
A	IPR014836	Integrin beta subunit, cytoplasmic domain	Domain
A	IPR012896	Integrin beta subunit, tail	Domain
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR032695	Integrin domain superfamily	Homologous Superfamily
A	IPR015812	Integrin beta subunit	Family
A	IPR002369	Integrin beta subunit, VWA domain	Domain
A	IPR016201	PSI domain	Domain
A	IPR015439	Integrin beta-2 superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P05107	leukocyte adhesion deficiency 1 acute promyelocytic leukemia Liver Cirrhosis, Experimental calcinosis leukocyte disease nephrosis dermatitis pneumonia heart valve disease leukocyte adhesion deficiency allergic disease Behcet disease Duchenne muscular dystrophy pneumonitis glioblastoma leukocyte adhesion deficiency 1 acute promyelocytic leukemia Liver Cirrhosis, Experimental calcinosis leukocyte disease nephrosis dermatitis pneumonia heart valve disease leukocyte adhesion deficiency allergic disease Behcet disease Duchenne muscular dystrophy pneumonitis glioblastoma Sjogren syndrome tuberculosis invasive ductal breast carcinoma acute myeloid leukemia astrocytic tumor lung carcinoma malignant mesothelioma cutaneous lupus erythematosus ovarian cancer Down syndrome pilocytic astrocytoma head and neck cancer IgA glomerulonephritis large cell medulloblastoma B-cell chronic lymphocytic leukemia malignant ependymoma brain cancer breast cancer pancreatic intraductal papillary-mucinous carcinoma dry eye syndrome gastric carcinoma subependymal giant cell astrocytoma interstitial cystitis ulcerative colitis lung cancer malignant glioma breast carcinoma chronic obstructive pulmonary disease osteosarcoma dermatomyositis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.