6T9E | pdb_00006t9e

Crystal structure of a bispecific DutaFab in complex with human PDGF

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D [auth DDD]	SCOP2B Superfamily	Cystine-knot cytokines	8038746	3000846	SCOP2B (2022-06-29)
C [auth CCC]	SCOP2B Superfamily	Cystine-knot cytokines	8038746	3000846	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)
D [auth DDD]	PG_binding_1	e6t9eDDD1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)
C [auth CCC]	PG_binding_1	e6t9eCCC1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)
F [auth LLL]	PG_binding_1	e6t9eLLL1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)
B [auth BBB]	PG_binding_1	e6t9eBBB1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)
E [auth HHH]	PG_binding_1	e6t9eHHH1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)
A [auth AAA]	PG_binding_1	e6t9eAAA1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth CCC], D [auth DDD]	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
C [auth CCC], D [auth DDD]	Platelet-derived growth factor subunit B	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor binding platelet-derived growth factor binding growth factor binding identical protein binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding 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 chemoattractant activity superoxide-generating NADPH oxidase activator activity enzyme regulator activity enzyme activator activity	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of biological process regulation of cellular process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion biological regulation developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of biological process regulation of cellular process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion biological regulation positive regulation of biological process cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion cellular process positive regulation of cellular process regulation of biosynthetic 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 chemotaxis positive regulation of locomotion response to stimulus regulation of response to external stimulus response to external stimulus regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus taxis regulation of response to stimulus response to chemical regulation of locomotion locomotion regulation of cell motility regulation of metanephric mesenchymal cell migration renal system development positive regulation of cell migration metanephros development positive regulation of cell motility regulation of cell migration cell migration cell migration involved in kidney development cell motility cell migration involved in metanephros development positive regulation of metanephric mesenchymal cell migration metanephric mesenchymal cell migration kidney development positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration smooth muscle cell migration muscle cell migration positive regulation of cell division cell division regulation of cell division positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process miRNA transcription regulation of miRNA metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of mitotic nuclear division positive regulation of mitotic nuclear division mitotic cell cycle cellular component organization regulation of mitotic cell cycle positive regulation of cell cycle process cellular component organization or biogenesis cell cycle regulation of cell cycle cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission positive regulation of nuclear division regulation of organelle organization positive regulation of cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division metanephric glomerulus vasculature development cellular developmental process connective tissue development metanephric glomerulus development metanephric glomerular mesangial cell development mesangial cell development cell development epithelial cell differentiation kidney vasculature development pericyte cell differentiation renal system vasculature development mesangial cell differentiation cell differentiation nephron development metanephric nephron development epithelial cell differentiation involved in kidney development blood vessel development epithelium development metanephric mesangial cell differentiation tissue development glomerular mesangium development glomerular mesangial cell development vasculature development glomerular mesangial cell differentiation glomerulus development metanephric glomerular mesangium development epithelial cell development cell differentiation involved in kidney development glomerulus vasculature development metanephric glomerular mesangial cell differentiation cellular response to stimulus cell surface receptor signaling pathway signaling platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway cell dedifferentiation involved in phenotypic switching regulation of developmental process vascular associated smooth muscle cell dedifferentiation reversible differentiation phenotypic switching dedifferentiation positive regulation of developmental process regulation of vascular associated smooth muscle cell dedifferentiation positive regulation of vascular associated smooth muscle cell dedifferentiation cell dedifferentiation cell chemotaxis cellular response to chemical stimulus renal system process system process regulation of renal system process regulation of system process regulation of glomerular filtration positive regulation of glomerular filtration positive regulation of multicellular organismal process regulation of multicellular organismal process glomerular filtration renal filtration protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process response to stress response to wounding regulation of calcium ion import regulation of calcium ion transport regulation of localization positive regulation of calcium ion transport positive regulation of calcium ion import transport regulation of transport regulation of monoatomic ion transport establishment of localization calcium ion transport metal ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport calcium ion import monoatomic cation transport regulation of metal ion transport 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 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 phospholipid metabolic process negative regulation of cellular process negative regulation of phospholipid biosynthetic process regulation of phosphatidylinositol biosynthetic process phosphatidylinositol metabolic process glycerophospholipid biosynthetic process negative regulation of phosphatidylinositol biosynthetic process negative regulation of metabolic process regulation of phospholipid metabolic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process regulation of phospholipid biosynthetic process negative regulation of phospholipid metabolic process glycerolipid biosynthetic process organophosphate metabolic process negative regulation of biosynthetic process organophosphate biosynthetic process negative regulation of phosphorus metabolic process glycerolipid metabolic process regulation of phosphorus metabolic process regulation of lipid biosynthetic process negative regulation of lipid metabolic process lipid metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of body fluid levels 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 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 cell activation 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 negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process platelet activation glycosaminoglycan metabolic process regulation of hyaluronan biosynthetic process carbohydrate derivative metabolic process regulation of polysaccharide metabolic process hyaluronan metabolic process polysaccharide metabolic process positive regulation of hyaluronan biosynthetic process glycosaminoglycan biosynthetic process regulation of carbohydrate metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process hyaluronan biosynthetic process regulation of polysaccharide biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process cellular response to endogenous stimulus cellular response to growth factor stimulus cellular response to platelet-derived growth factor stimulus response to endogenous stimulus response to growth factor response to platelet-derived growth factor positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction 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 anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis reactive oxygen species metabolic process 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 platelet-derived growth factor receptor-beta signaling pathway positive regulation of glomerular mesangial cell proliferation regulation of glomerular mesangial cell proliferation positive regulation of cell proliferation involved in kidney development cell proliferation involved in kidney development glomerular mesangial cell proliferation fibroblast proliferation regulation of fibroblast proliferation positive regulation of fibroblast proliferation regulation of vascular associated smooth muscle cell proliferation positive regulation of vascular associated smooth muscle cell proliferation vascular associated smooth muscle cell proliferation cell-cell signaling paracrine signaling 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 placenta development chordate embryonic development embryo development in utero embryonic development embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process regulation of vascular associated smooth muscle cell migration vascular associated smooth muscle cell migration positive regulation of vascular associated smooth muscle cell migration negative regulation of miRNA transcription negative regulation of miRNA metabolic process peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration blood vessel endothelial cell migration regulation of endothelial cell migration positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity positive regulation of protein phosphorylation positive regulation of MAP kinase activity positive regulation of phosphorus metabolic process regulation of protein metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of molecular function positive regulation of protein modification process positive regulation of protein kinase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of phosphorylation monocyte chemotaxis leukocyte migration immune system process mononuclear cell migration myeloid leukocyte migration leukocyte chemotaxis response to mycophenolic acid response to oxygen-containing compound cellular response to mycophenolic acid cellular response to oxygen-containing compound regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process DNA metabolic process positive regulation of DNA metabolic process DNA biosynthetic process regulation of DNA metabolic process muscle adaptation smooth muscle adaptation muscle system process smooth muscle cell differentiation regulation of smooth muscle cell differentiation negative regulation of muscle cell differentiation regulation of cell differentiation muscle cell differentiation muscle structure development vascular associated smooth muscle cell differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of vascular associated smooth muscle cell differentiation regulation of vascular associated smooth muscle cell differentiation negative regulation of smooth muscle cell differentiation regulation of muscle cell differentiation negative regulation of gene expression endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation cellular response to interleukin-18 response to interleukin-18 response to cytokine cytokine-mediated signaling pathway interleukin-18-mediated signaling pathway response to peptide cellular response to cytokine stimulus	cell periphery cellular anatomical structure basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane intracellular anatomical structure cytoplasm platelet-derived growth factor complex protein-containing complex growth factor complex membrane-bounded organelle cell periphery cellular anatomical structure basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane intracellular anatomical structure cytoplasm platelet-derived growth factor complex protein-containing complex growth factor complex membrane-bounded organelle membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum Golgi membrane Golgi apparatus bounding membrane of organelle organelle membrane 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 extracellular matrix external encapsulating structure Golgi lumen
B [auth BBB], F [auth LLL]	DutaFab mat VL chain	-	-	-
A [auth AAA], E [auth HHH]	DutaFab mat VH chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth CCC], D [auth DDD]	Pharos: P01127	dermatofibrosarcoma protuberans basal ganglia calcification, idiopathic, 5 familial meningioma essential thrombocythemia basal ganglia calcification, idiopathic, 1 bilateral striopallidodentate calcinosis pulmonary fibrosis Fibrosis calcinosis retinal disease basal ganglia disease idiopathic interstitial pneumonia lymphoplasmacyte-rich meningioma pigmented dermatofibrosarcoma protuberans secretory meningioma dermatofibrosarcoma protuberans basal ganglia calcification, idiopathic, 5 familial meningioma essential thrombocythemia basal ganglia calcification, idiopathic, 1 bilateral striopallidodentate calcinosis pulmonary fibrosis Fibrosis calcinosis retinal disease basal ganglia disease idiopathic interstitial pneumonia lymphoplasmacyte-rich meningioma pigmented dermatofibrosarcoma protuberans secretory meningioma ulcerative colitis inflammatory bowel disease malignant mesothelioma plasma cell myeloma Crohn disease hepatocellular carcinoma intellectual disability lung cancer meningioma primary biliary cholangitis cancer rheumatoid arthritis fibrosarcoma

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.