1VCA | pdb_00001vca

CRYSTAL STRUCTURE OF AN INTEGRIN-BINDING FRAGMENT OF VASCULAR CELL ADHESION MOLECULE-1 AT 1.8 ANGSTROMS RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1vcaa1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C2 set domains	Vascular cell adhesion molecule-1 (VCAM-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1vcaa2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Vascular cell adhesion molecule-1 (VCAM-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1vcab1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C2 set domains	Vascular cell adhesion molecule-1 (VCAM-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1vcab2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Vascular cell adhesion molecule-1 (VCAM-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	C2 set domains	8054732	4007529	SCOP2 (2022-06-29)
A	SCOP2 Family	I set domains	8054752	4007543	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054733	3000071	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054753	3000071	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054753	3000071	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054733	3000071	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	C2-set	e1vcaA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C2-set	ECOD (1.6)
A	I-set_5	e1vcaA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)
B	C2-set	e1vcaB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C2-set	ECOD (1.6)
B	I-set_5	e1vcaB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A, B	VCAM1	2C-LIKE	Homo sapiens (human)	VCAM1*01	C-LIKE-DOMAIN C-LIKE	RPI	2C-LIKE	IMGT (202510-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05790	Immunoglobulin C2-set domain (C2-set)	Immunoglobulin C2-set domain		Domain
A, B	PF07679	Immunoglobulin I-set domain (I-set)	Immunoglobulin I-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	HUMAN VASCULAR CELL ADHESION MOLECULE-1	cell adhesion molecule binding protein binding binding cell adhesion mediator activity protein-containing complex binding integrin binding signaling receptor binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor primary methylamine oxidase activity catalytic activity	leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration cell adhesion cell-cell adhesion immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cellular process cell motility membrane to membrane docking membrane docking amine metabolic process leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration cell adhesion cell-cell adhesion immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cellular process cell motility membrane to membrane docking membrane docking amine metabolic process metabolic process heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell-cell adhesion via plasma-membrane adhesion molecules response to stimulus response to metal ion response to chemical response to zinc ion response to ionizing radiation response to radiation response to abiotic stimulus cell chemotaxis cellular response to stimulus chemotaxis response to external stimulus cellular response to chemical stimulus taxis locomotion response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels heterotypic cell-cell adhesion multicellular organismal process regulation of cellular process positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process regulation of leukocyte proliferation regulation of biological process cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of multicellular organismal process positive regulation of biological process positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte proliferation leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of mononuclear cell proliferation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion biological regulation cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus response to growth factor cell-cell adhesion mediated by integrin cell adhesion mediated by integrin cell-matrix adhesion cell-substrate adhesion developmental process cellular developmental process hemopoiesis B cell activation cell development mononuclear cell differentiation lymphocyte differentiation B cell differentiation cell differentiation anatomical structure development leukocyte differentiation chronic inflammatory response defense response inflammatory response heart development animal organ development peripheral nervous system development cardiac neuron differentiation nervous system development cardiocyte differentiation circulatory system development peripheral nervous system neuron differentiation generation of neurons multicellular organism development neurogenesis neuron differentiation autonomic nervous system development system development response to alcohol response to oxygen-containing compound response to ethanol response to peptide cellular response to tumor necrosis factor response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor response to nutrient levels response to nutrient response to nicotine nerve development innervation cellular response to nitrogen compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound response to amyloid-beta biological process involved in interspecies interaction between organisms response to lipid response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex cell surface external side of plasma membrane side of membrane apical part of cell intracellular organelle intracellular anatomical structure cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex cell surface external side of plasma membrane side of membrane apical part of cell intracellular organelle intracellular anatomical structure podosome cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle sarcolemma Golgi apparatus cytoplasm intracellular membrane-bounded organelle endomembrane system cell projection actin-based cell projection microvillus plasma membrane bounded cell projection filopodium early endosome endosome intracellular vesicle cytoplasmic vesicle endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR013106	Immunoglobulin V-set domain	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR008424	Immunoglobulin C2-set	Domain
A, B	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR003598	Immunoglobulin subtype 2	Domain
A, B	IPR013098	Immunoglobulin I-set	Domain
A, B	IPR047012	Intercellular adhesion molecule/vascular cell adhesion molecule	Family
A, B	IPR003987	Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal	Domain
A, B	IPR003989	Vascular cell adhesion molecule-1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P19320	ulcerative colitis sickle cell anemia hypertensive disorder atherosclerosis uremia Hypercholesterolemia urticaria cholestasis dermatitis cardiovascular disease multiple sclerosis coronary artery disease Duchenne muscular dystrophy thrombotic disease glioblastoma ulcerative colitis sickle cell anemia hypertensive disorder atherosclerosis uremia Hypercholesterolemia urticaria cholestasis dermatitis cardiovascular disease multiple sclerosis coronary artery disease Duchenne muscular dystrophy thrombotic disease glioblastoma arteriosclerosis disorder intrahepatic cholestasis breast cancer malignant mesothelioma cerebrovascular disorder chronic obstructive pulmonary disease osteosarcoma cutaneous lupus erythematosus pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor Emery-Dreifuss muscular dystrophy Sjogren syndrome type 2 diabetes mellitus head and neck cancer arthritic joint disease juvenile dermatomyositis malignant ependymoma cancer medulloblastoma myocardial ischemia congenital diaphragmatic hernia ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sarcoidosis esophageal adenocarcinoma subependymal giant cell astrocytoma gastric carcinoma hepatocellular carcinoma inborn carbohydrate metabolic disorder astrocytic tumor kidney disease autoimmune disease malignant glioma myopathy pancreatic ductal adenocarcinoma diabetes mellitus pituitary cancer

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.