3MJK | pdb_00003mjk

Structure of a growth factor precursor

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth Y]	PDGF	e3mjkY1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PDGF	ECOD (1.6)
E [auth X]	PDGF	e3mjkX1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PDGF	ECOD (1.6)
D [auth F]	PDGF	e3mjkF1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PDGF	ECOD (1.6)
C [auth E]	PDGF	e3mjkE1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PDGF	ECOD (1.6)
B	PDGF	e3mjkB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PDGF	ECOD (1.6)
A	PDGF	e3mjkA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PDGF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth Y]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
E [auth X]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
D [auth F]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
C [auth E]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
B	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
A	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth E], D [auth F], E [auth X], A, B, C [auth E], D [auth F], E [auth X], F [auth Y]	PF00341	PDGF/VEGF domain (PDGF)	PDGF/VEGF domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth E], D [auth F], E [auth X], A, B, C [auth E], D [auth F], E [auth X], F [auth Y]	Platelet-derived growth factor subunit A	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity platelet-derived growth factor receptor binding growth factor receptor binding platelet-derived growth factor binding growth factor binding identical protein binding protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity platelet-derived growth factor receptor binding growth factor receptor binding platelet-derived growth factor binding growth factor binding identical protein binding protein heterodimerization activity protein dimerization activity collagen binding protein-containing complex binding protein homodimerization activity	multicellular organismal process cell activation cellular process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus platelet-derived growth factor receptor-alpha signaling pathway signaling platelet-derived growth factor receptor signaling pathway biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication multicellular organismal process cell activation cellular process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus platelet-derived growth factor receptor-alpha signaling pathway signaling platelet-derived growth factor receptor signaling pathway biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway cell population proliferation developmental process multicellular organism development skeletal system development anatomical structure development animal organ development bone development system development cell-cell signaling cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization positive regulation of cell division positive regulation of biological process cell division positive regulation of cellular process regulation of cell division regulation of cell motility regulation of smooth muscle cell migration smooth muscle cell migration muscle cell migration regulation of locomotion regulation of cell migration cell migration cell motility locomotion chemotaxis negative chemotaxis taxis response to chemical response to external stimulus response to stress response to wounding regulation of lipid metabolic process glycerophospholipid metabolic process negative regulation of biological process lipid biosynthetic process negative regulation of phosphate metabolic process negative regulation of lipid biosynthetic process regulation of primary metabolic process phospholipid metabolic process phosphate-containing compound metabolic process negative regulation of cellular process negative regulation of phospholipid biosynthetic process phosphorus metabolic process regulation of phosphatidylinositol biosynthetic process regulation of biosynthetic process phosphatidylinositol metabolic process glycerophospholipid biosynthetic process negative regulation of phosphatidylinositol biosynthetic process negative regulation of metabolic process regulation of phospholipid metabolic process primary metabolic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process regulation of phospholipid biosynthetic process negative regulation of phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process negative regulation of biosynthetic process organophosphate biosynthetic process negative regulation of phosphorus metabolic process metabolic process glycerolipid metabolic process regulation of phosphorus metabolic process regulation of lipid biosynthetic process regulation of metabolic process negative regulation of lipid metabolic process lipid metabolic process regulation of body fluid levels regulation of response to external stimulus regulation of cell activation negative regulation of platelet activation regulation of response to wounding regulation of coagulation regulation of response to stress coagulation regulation of multicellular organismal process regulation of biological quality regulation of hemostasis wound healing negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation hemostasis negative regulation of response to wounding blood coagulation negative regulation of cell activation negative regulation of hemostasis regulation of platelet activation negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process platelet activation anatomical structure morphogenesis animal organ morphogenesis positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development positive regulation of locomotion regulation of metanephric mesenchymal cell migration renal system development positive regulation of cell migration metanephros development positive regulation of cell motility positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway cell migration involved in kidney development platelet-derived growth factor receptor-beta signaling pathway cell migration involved in metanephros development positive regulation of metanephric mesenchymal cell migration metanephric mesenchymal cell migration kidney development skin development regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process regulation of organelle organization regulation of actin cytoskeleton organization fibroblast proliferation positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation digestive system development digestive tract development epithelium development epidermis development molting cycle process hair cycle tissue development skin epidermis development hair follicle development molting cycle hair cycle process positive regulation of mesenchymal cell proliferation regulation of mesenchymal cell proliferation mesenchymal cell proliferation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction cellular component biogenesis cellular component assembly cell projection organization cell projection assembly embryonic organ development embryo development embryonic lung development regulation of developmental process gland development branching involved in salivary gland morphogenesis epithelial-mesenchymal cell signaling gland morphogenesis salivary gland morphogenesis regulation of branching involved in salivary gland morphogenesis regulation of morphogenesis of an epithelium regulation of anatomical structure morphogenesis regulation of morphogenesis of a branching structure regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling regulation of animal organ morphogenesis morphogenesis of an epithelium salivary gland development tissue morphogenesis morphogenesis of a branching structure exocrine system development morphogenesis of a branching epithelium respiratory tube development lung development respiratory system development lung alveolus development positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation protein modification process protein phosphorylation positive regulation of phosphorus metabolic process protein autophosphorylation phosphorylation regulation of protein metabolic process regulation of macromolecule metabolic process regulation of protein autophosphorylation macromolecule modification regulation of phosphorylation macromolecule metabolic process positive regulation of protein autophosphorylation	platelet-derived growth factor complex protein-containing complex growth factor complex membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle platelet-derived growth factor complex protein-containing complex growth factor complex membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm Golgi membrane Golgi apparatus membrane bounding membrane of organelle organelle membrane cell projection actin-based cell projection microvillus plasma membrane bounded cell projection vesicle lumen intracellular vesicle cytoplasmic vesicle lumen secretory granule lumen cytoplasmic vesicle secretory granule secretory vesicle platelet alpha granule vesicle platelet alpha granule lumen extracellular region extracellular space cell surface Golgi lumen cell periphery platelet-derived growth factor receptor-ligand complex plasma membrane protein complex plasma membrane membrane protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth E], D [auth F], E [auth X], A, B, C [auth E], D [auth F], E [auth X], F [auth Y]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B, C [auth E], D [auth F], E [auth X], A, B, C [auth E], D [auth F], E [auth X], F [auth Y]	IPR006782	Platelet-derived growth factor, N-terminal	Domain
A, B, C [auth E], D [auth F], E [auth X], A, B, C [auth E], D [auth F], E [auth X], F [auth Y]	IPR023581	Platelet-derived growth factor, conserved site	Conserved Site
A, B, C [auth E], D [auth F], E [auth X], A, B, C [auth E], D [auth F], E [auth X], F [auth Y]	IPR000072	PDGF/VEGF domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C [auth E], D [auth F], E [auth X], A, B, C [auth E], D [auth F], E [auth X], F [auth Y]	Pharos: P04085	breast carcinoma essential thrombocythemia Liver Cirrhosis, Experimental breast cancer pulmonary fibrosis carcinoma thyroid adenoma amyotrophic lateral sclerosis type 1 sarcomatoid carcinoma thyroid gland carcinoma hydrolethalus syndrome lung disease atypical teratoid rhabdoid tumor oligodendroglioma pancreatic ductal adenocarcinoma breast carcinoma essential thrombocythemia Liver Cirrhosis, Experimental breast cancer pulmonary fibrosis carcinoma thyroid adenoma amyotrophic lateral sclerosis type 1 sarcomatoid carcinoma thyroid gland carcinoma hydrolethalus syndrome lung disease atypical teratoid rhabdoid tumor oligodendroglioma pancreatic ductal adenocarcinoma esophageal adenocarcinoma glioblastoma idiopathic interstitial pneumonia lung adenocarcinoma malignant pancreatic neoplasm mammary neoplasms, animal medulloblastoma osteosarcoma benign mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia thyroid cancer undifferentiated carcinoma large cell medulloblastoma lung cancer malignant mesothelioma astrocytic tumor mesothelioma ovarian cancer psoriasis breast fibroadenoma cystic fibrosis exocrine pancreatic carcinoma

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.