4NEN | pdb_00004nen

An internal ligand-bound, metastable state of a leukocyte integrin, aXb2

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	8044051	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)
A	CBS	e4nenA1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (develop294)
B	2OG-FeII_Oxy_2	e4nenB1	A: alpha bundles	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: 2OG-FeII_Oxy_2	ECOD (develop294)
B	CoV_NSP4_C	e4nenB8	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: CoV_NSP4_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
A	2.60.40.1460	Mainly Beta	Sandwich	Immunoglobulin-like	Integrin domains. Chain A, domain 2	CATH (4.3.0)
A	2.60.40.1510	Mainly Beta	Sandwich	Immunoglobulin-like	ntegrin, alpha v. Chain A, domain 3	CATH (4.3.0)
A	2.60.40.1530	Mainly Beta	Sandwich	Immunoglobulin-like	ntegrin, alpha v. Chain A, domain 4	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21520	Integrin alpha-X-like, Ig-like domain 3 (ITGAX-like_Ig_3)	Integrin alpha-X-like, Ig-like domain 3	This domain is found in Integrin alpha-X from humans (ITGAX) and similar proteins predominantly found in vertebrates. ITGAX is a receptor for fibrinogen. This region composed of an immunoglobulin-like domain [1,3].	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
B	PF23105	Integrin EGF domain (EGF_integrin)	Integrin EGF domain	This entry represents an EGF that is found in several integrin proteins.	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
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	PF07965	Integrin beta tail domain (Integrin_B_tail)	Integrin beta tail domain	This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Integrin alpha-X	molecular transducer activity signaling receptor activity cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding enzyme binding protein kinase binding cation binding molecular transducer activity signaling receptor activity cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding enzyme binding protein kinase binding cation binding ion binding metal ion binding small molecule binding	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular response to stimulus integrin-mediated signaling pathway cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation multicellular organismal process system process regulation of developmental process regulation of myelination regulation of system process regulation of nervous system development multicellular organism development positive regulation of myelination axon ensheathment ensheathment of neurons positive regulation of nervous system process regulation of multicellular organismal process system development regulation of multicellular organismal development nervous system process nervous system development regulation of nervous system process myelination positive regulation of multicellular organismal process angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion endothelium development morphogenesis of an endothelium regulation of endothelial tube morphogenesis positive regulation of morphogenesis of an epithelium regulation of morphogenesis of an epithelium epithelial tube morphogenesis epithelium development positive regulation of endothelial tube morphogenesis morphogenesis of an epithelium endothelial tube morphogenesis tissue development tissue morphogenesis cell-cell adhesion heterotypic cell-cell adhesion biological process involved in interspecies interaction between organisms defense response to virus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule 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 cell periphery cell surface plasma membrane external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex membrane protein complex receptor complex integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion integrin alphaX-beta2 complex ficolin-1-rich granule membrane ficolin-1-rich granule
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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013517	FG-GAP repeat	Repeat
A	IPR013519	Integrin alpha beta-propellor	Repeat
A	IPR000413	Integrin alpha chain	Family
A	IPR048633	Integrin alpha-X-like, third Ig-like domain	Domain
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
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P20702	acute promyelocytic leukemia IgA glomerulonephritis systemic lupus erythematosus colitis facioscapulohumeral muscular dystrophy invasive ductal breast carcinoma MALT lymphoma psoriasis systemic sclerosis autoimmune disease cutaneous lupus erythematosus glioblastoma influenza lung carcinoma non-small cell lung carcinoma acute promyelocytic leukemia IgA glomerulonephritis systemic lupus erythematosus colitis facioscapulohumeral muscular dystrophy invasive ductal breast carcinoma MALT lymphoma psoriasis systemic sclerosis autoimmune disease cutaneous lupus erythematosus glioblastoma influenza lung carcinoma non-small cell lung carcinoma skin disease cancer ductal breast carcinoma in situ hematologic disease interstitial cystitis malignant mesothelioma osteosarcoma
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 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 brain cancer malignant ependymoma 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