6NDB | pdb_00006ndb

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND COBALT

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)
R	SCOP2B Superfamily	vWA-like	8041194	3000832	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	vWA-like	8041194	3000832	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	vWA-like	8041194	3000832	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	vWA-like	8041194	3000832	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	vWA-like	8041194	3000832	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	vWA-like	8041194	3000832	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	C-type lectin-like	8065482	3001261	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	C-type lectin-like	8065482	3001261	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	C-type lectin-like	8065482	3001261	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	C-type lectin-like	8065482	3001261	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	C-type lectin-like	8065482	3001261	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-type lectin-like	8065482	3001261	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	C-type lectin-like	8065524	3001261	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	C-type lectin-like	8065524	3001261	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	C-type lectin-like	8065524	3001261	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	C-type lectin-like	8065524	3001261	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	C-type lectin-like	8065524	3001261	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C-type lectin-like	8065524	3001261	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)
R	C1-set	e6ndbR1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
O	C1-set	e6ndbO1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
L	C1-set	e6ndbL1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
I	C1-set	e6ndbI1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
F	C1-set	e6ndbF1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
C	C1-set	e6ndbC1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
Q	C1-set	e6ndbQ1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
N	C1-set	e6ndbN1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
K	C1-set	e6ndbK1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
H	C1-set	e6ndbH1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
E	C1-set	e6ndbE1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
B	C1-set	e6ndbB1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
P	C1-set	e6ndbP1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
M	C1-set	e6ndbM1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
J	C1-set	e6ndbJ1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
G	C1-set	e6ndbG1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
D	C1-set	e6ndbD1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)
A	C1-set	e6ndbA1	A: beta barrels	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: C1-set	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
R	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
O	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
L	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
I	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
F	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
C	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
Q	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
N	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
K	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
H	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
E	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
B	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
P	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
M	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
J	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
G	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
D	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
A	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L, O C, F, I, L, O, R	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L, O C, F, I, L, O, R	Integrin alpha-2	amyloid-beta binding binding peptide binding cell adhesion molecule binding collagen binding protein-containing complex binding collagen binding involved in cell-matrix adhesion protein binding cell adhesion mediator activity cell-matrix adhesion mediator activity extracellular matrix binding laminin binding molecular transducer activity collagen receptor activity amyloid-beta binding binding peptide binding cell adhesion molecule binding collagen binding protein-containing complex binding collagen binding involved in cell-matrix adhesion protein binding cell adhesion mediator activity cell-matrix adhesion mediator activity extracellular matrix binding laminin binding molecular transducer activity collagen receptor activity transmembrane signaling receptor activity signaling receptor activity cation binding ion binding metal ion binding small molecule binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding virus receptor activity exogenous protein binding integrin binding signaling receptor binding	response to stimulus response to activity response to muscle activity response to chemical response to xenobiotic stimulus multicellular organismal process regulation of body fluid levels wound healing hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to stimulus response to activity response to muscle activity response to chemical response to xenobiotic stimulus multicellular organismal process regulation of body fluid levels wound healing hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding positive regulation of cell communication regulation of biological process system process regulation of cellular process nervous system process regulation of system process positive regulation of biological process positive regulation of transmission of nerve impulse transmission of nerve impulse regulation of nervous system process cell communication regulation of transmission of nerve impulse positive regulation of nervous system process positive regulation of multicellular organismal process regulation of cell communication regulation of multicellular organismal process cellular process positive regulation of cellular process response to nutrient levels response to monosaccharide response to carbohydrate response to nutrient response to oxygen-containing compound response to L-ascorbic acid response to vitamin cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization developmental process mammary gland development gland development animal organ development anatomical structure development positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion epithelium development cellular developmental process tissue development liver development epithelial cell differentiation multicellular organism development cell differentiation hepaticobiliary system development hepatocyte differentiation system development cell adhesion cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus focal adhesion assembly cell-substrate junction assembly cell-substrate adhesion cellular component biogenesis cell junction organization cellular component assembly cell-matrix adhesion cell junction assembly cell-substrate junction organization anatomical structure morphogenesis skin development skin morphogenesis animal organ morphogenesis cellular response to stimulus cell surface receptor signaling pathway signaling signal transduction collagen-activated signaling pathway regulation of biosynthetic process collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of metabolic process positive regulation of collagen metabolic process biosynthetic process positive regulation of biosynthetic process positive regulation of collagen biosynthetic process metabolic process collagen metabolic process regulation of metabolic process positive regulation of cellular component organization regulation of cellular component organization cell projection organization regulation of cell projection organization positive regulation of cell projection organization response to parathyroid hormone response to hormone response to endogenous stimulus detection of external stimulus detection of mechanical stimulus involved in sensory perception of pain response to mechanical stimulus response to external stimulus sensory perception of pain detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of mechanical stimulus detection of stimulus involved in sensory perception multi-multicellular organism process reproductive process female pregnancy multi-organism reproductive process import into cell regulation of localization transport positive regulation of membrane invagination vesicle-mediated transport localization positive regulation of endocytosis regulation of phagocytosis, engulfment membrane invagination phagocytosis plasma membrane invagination regulation of endocytosis membrane organization regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization phagocytosis, engulfment positive regulation of phagocytosis positive regulation of transport positive regulation of phagocytosis, engulfment regulation of membrane invagination endocytosis integrin-mediated signaling pathway cell adhesion mediated by integrin positive regulation of cell adhesion regulation of cell adhesion positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process macromolecule metabolic process substrate-dependent cell migration regulation of leukocyte migration positive regulation of leukocyte migration leukocyte migration immune system process regulation of immune system process positive regulation of immune system process positive chemotaxis chemotaxis regulation of response to external stimulus positive regulation of positive chemotaxis regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus regulation of positive chemotaxis positive regulation of response to external stimulus taxis regulation of response to stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus response to osmotic stress hypotonic response positive regulation of smooth muscle contraction muscle contraction muscle system process regulation of muscle system process smooth muscle contraction regulation of muscle contraction regulation of smooth muscle contraction positive regulation of muscle contraction response to lipid cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to lipid response to estradiol cellular response to estradiol stimulus formation of primary germ layer mesodermal cell differentiation mesoderm morphogenesis embryonic morphogenesis embryo development gastrulation tissue morphogenesis anatomical structure formation involved in morphogenesis mesoderm formation mesoderm development cell-cell adhesion response to amine response to nitrogen compound positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration epithelial cell migration regulation of epithelial cell migration epithelium migration	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure perinuclear region of cytoplasm cytoplasm anchoring junction cell junction focal adhesion cell-substrate junction cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure perinuclear region of cytoplasm cytoplasm anchoring junction cell junction focal adhesion cell-substrate junction protein-containing complex plasma membrane protein complex membrane protein complex integrin complex plasma membrane signaling receptor complex signaling receptor complex protein complex involved in cell adhesion basal part of cell integrin alpha2-beta1 complex axon synapse neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon neuron projection terminus
B, E, H, K, N B, E, H, K, N, Q	Snaclec rhodocetin subunit delta	toxin activity	-	cellular anatomical structure extracellular region
A, D, G, J, M A, D, G, J, M, P	Snaclec rhodocetin subunit gamma	toxin activity	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L, O C, F, I, L, O, R	IPR013517	FG-GAP repeat	Repeat
C, F, I, L, O C, F, I, L, O, R	IPR048286	Integrin alpha, third immunoglobulin-like domain	Domain
C, F, I, L, O C, F, I, L, O, R	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
C, F, I, L, O C, F, I, L, O, R	IPR002035	von Willebrand factor, type A	Domain
C, F, I, L, O C, F, I, L, O, R	IPR048285	Integrin alpha, second immunoglobulin-like domain	Domain
C, F, I, L, O C, F, I, L, O, R	IPR032695	Integrin domain superfamily	Homologous Superfamily
C, F, I, L, O C, F, I, L, O, R	IPR013519	Integrin alpha beta-propellor	Repeat
C, F, I, L, O C, F, I, L, O, R	IPR000413	Integrin alpha chain	Family
C, F, I, L, O C, F, I, L, O, R	IPR028994	Integrin alpha, N-terminal	Homologous Superfamily
C, F, I, L, O C, F, I, L, O, R	IPR018184	Integrin alpha chain, C-terminal cytoplasmic region, conserved site	Conserved Site
B, E, H, K, N B, E, H, K, N, Q	IPR001304	C-type lectin-like	Domain
B, E, H, K, N B, E, H, K, N, Q	IPR018378	C-type lectin, conserved site	Conserved Site
B, E, H, K, N B, E, H, K, N, Q	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
B, E, H, K, N B, E, H, K, N, Q	IPR050111	C-type lectin and snaclec domain-containing protein	Family
B, E, H, K, N B, E, H, K, N, Q	IPR016187	C-type lectin fold	Homologous Superfamily
A, D, G, J, M A, D, G, J, M, P	IPR001304	C-type lectin-like	Domain
A, D, G, J, M A, D, G, J, M, P	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
A, D, G, J, M A, D, G, J, M, P	IPR050111	C-type lectin and snaclec domain-containing protein	Family
A, D, G, J, M A, D, G, J, M, P	IPR016187	C-type lectin fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F, I, L, O C, F, I, L, O, R	: P17301	retinal vein occlusion Hyperalgesia endometriosis platelet-type bleeding disorder 9 malignant mesothelioma myocardial infarction osteosarcoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor breast cancer glioblastoma malignant ependymoma malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm retinal vein occlusion Hyperalgesia endometriosis platelet-type bleeding disorder 9 malignant mesothelioma myocardial infarction osteosarcoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor breast cancer glioblastoma malignant ependymoma malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm progressive supranuclear palsy chronic obstructive pulmonary disease IgA glomerulonephritis malignant glioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor ulcerative colitis cystic fibrosis lung carcinoma

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.