5E6U | pdb_00005e6u

Structures of leukocyte integrin aLb2: The aI domain, the headpiece, and the pocket for the internal ligand

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	vWA-like	8042676	3000832	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e5e6uB1	A: Alpha-beta plaits	X: Pseudouridine synthase	H: Pseudouridine synthase	T: MG2	F:	ECOD (20:10:01)
A		e5e6uA1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: Ribosomal_S5_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	CATH (4.3.0)
B	2.60.40.1510	Mainly Beta	Sandwich	Immunoglobulin-like	ntegrin, alpha v. Chain A, domain 3	CATH (4.3.0)
B	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
A	2.130.10.130	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	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
B	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
A	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain		Domain
A	PF01839	FG-GAP repeat (FG-GAP)	FG-GAP repeat	-	Repeat
A	PF08441	Integrin alpha Ig-like domain 1 (Integrin_A_Ig_1)	Integrin alpha Ig-like domain 1	This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of Pfam:PF01839 repeats and to the N-terminus of the Pfam:PF00357 cytoplasmic region. This region is composed of an immunoglobulin-like domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Integrin beta-2	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 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 biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process positive regulation of cellular process reactive oxygen species metabolic process regulation of superoxide metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process superoxide anion generation positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of reactive oxygen species metabolic 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 endothelial cell migration cell migration cell motility regulation of protein modification process regulation of protein phosphorylation peptidyl-tyrosine modification regulation of primary metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus 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 leukocyte chemotaxis locomotion apoptotic process cell death programmed cell death signaling cell-cell signaling cell communication cellular extravasation defense response response to stress inflammatory response leukocyte migration involved in inflammatory response cellular response to low-density lipoprotein particle stimulus response to endogenous stimulus response to lipoprotein particle cellular response to lipoprotein particle stimulus cell adhesion negative regulation of dopamine metabolic process regulation of amine metabolic process negative regulation of metabolic process negative regulation of biological process dopamine metabolic process catechol-containing compound metabolic process amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process negative regulation of cellular process negative regulation of amine metabolic process regulation of catecholamine metabolic process biogenic amine metabolic process regulation of dopamine 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 regulated secretory pathway positive regulation of immune response 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 regulation of regulated secretory pathway positive regulation of response to stimulus 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 receptor clustering macromolecule localization intracellular protein localization localization within membrane protein localization to membrane macrophage activation leukocyte activation involved in inflammatory response microglial cell activation 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 establishment of protein localization to membrane regulation of establishment of protein localization protein targeting to membrane regulation of cellular localization regulation of protein targeting positive regulation of protein targeting to membrane 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 cell adhesion mediated by integrin regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of multicellular organismal process blood vessel development system development regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process 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 intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure 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 alphaD-beta2 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
A	Integrin alpha-L	molecular transducer activity signaling receptor activity cell adhesion molecule binding protein binding binding ICAM-3 receptor activity transmembrane signaling receptor activity protein-containing complex binding cation binding ion binding metal ion binding small molecule binding	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process T cell extravasation lymphocyte migration memory T cell extravasation leukocyte migration immune system process mononuclear cell migration cellular extravasation cell migration cell motility T cell migration cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process T cell extravasation lymphocyte migration memory T cell extravasation leukocyte migration immune system process mononuclear cell migration cellular extravasation cell migration cell motility T cell migration localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process integrin-mediated signaling pathway regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication signal transduction heterophilic cell-cell adhesion cell-cell adhesion leukocyte cell-cell adhesion defense response response to stress inflammatory response cellular localization receptor clustering macromolecule localization intracellular protein localization localization within membrane protein localization to membrane multicellular organismal process immune response cell activation lymphocyte activation cell activation involved in immune response leukocyte activation immune effector process T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell T cell activation involved in immune response T cell activation leukocyte activation involved in immune response lymphocyte activation involved in immune response	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell surface protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex receptor complex cell periphery integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion integrin alphaL-beta2 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR033760	Integrin beta N-terminal	Domain
B	IPR036349	Integrin beta tail domain superfamily	Homologous Superfamily
B	IPR014836	Integrin beta subunit, cytoplasmic domain	Domain
B	IPR012896	Integrin beta subunit, tail	Domain
B	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B	IPR057073	Integrin beta, epidermal growth factor-like domain 2	Domain
B	IPR032695	Integrin domain superfamily	Homologous Superfamily
B	IPR015812	Integrin beta subunit	Family
B	IPR057243	Integrins beta, I-EGF domain, conserved site	Conserved Site
B	IPR002369	Integrin beta subunit, VWA domain	Domain
B	IPR016201	PSI domain	Domain
B	IPR015439	Integrin beta-2 superfamily	Homologous Superfamily
A	IPR013517	FG-GAP repeat	Repeat
A	IPR013519	Integrin alpha beta-propellor	Repeat
A	IPR000413	Integrin alpha chain	Family
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR013649	Integrin alpha, first immunoglubulin-like domain	Domain
A	IPR028994	Integrin alpha, N-terminal	Homologous Superfamily
A	IPR002035	von Willebrand factor, type A	Domain
A	IPR048285	Integrin alpha, second immunoglobulin-like domain	Domain
A	IPR032695	Integrin domain superfamily	Homologous Superfamily
A	IPR018184	Integrin alpha chain, C-terminal cytoplasmic region, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	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 pneumonitis Duchenne muscular dystrophy Sjogren syndrome 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 pneumonitis Duchenne muscular dystrophy Sjogren syndrome glioblastoma tuberculosis invasive ductal breast carcinoma acute myeloid leukemia astrocytic tumor lung carcinoma malignant mesothelioma ovarian cancer cutaneous lupus erythematosus pilocytic astrocytoma Down syndrome head and neck cancer IgA glomerulonephritis large cell medulloblastoma B-cell chronic lymphocytic leukemia brain cancer malignant ependymoma breast cancer pancreatic intraductal papillary-mucinous carcinoma dry eye syndrome gastric carcinoma subependymal giant cell astrocytoma ulcerative colitis interstitial cystitis lung cancer malignant glioma breast carcinoma osteosarcoma chronic obstructive pulmonary disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia dermatomyositis
A	Pharos: P20701	ulcerative colitis acute promyelocytic leukemia Liver Cirrhosis, Experimental Behcet disease inflammatory bowel disease Sjogren syndrome chronic obstructive pulmonary disease dry eye syndrome interstitial cystitis lung carcinoma osteosarcoma spina bifida atopic eczema glioblastoma malignant glioma ulcerative colitis acute promyelocytic leukemia Liver Cirrhosis, Experimental Behcet disease inflammatory bowel disease Sjogren syndrome chronic obstructive pulmonary disease dry eye syndrome interstitial cystitis lung carcinoma osteosarcoma spina bifida atopic eczema glioblastoma malignant glioma periodontitis psoriasis tuberculosis cutaneous lupus erythematosus lung cancer non-small cell lung carcinoma pilocytic astrocytoma