4QCI

PDGF-B blocking antibody bound to PDGF-BB

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab 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	d4qcia1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d4qcil1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4qcib_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth H]	d4qcih_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4qcic_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Platelet-derived growth factor-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4qcid_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Platelet-derived growth factor-like	automated matches	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)
C	SCOP2B Superfamily	Cystine-knot cytokines	8038746	3000846	SCOP2B (2022-06-29)
D	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)
A	C1-set_1	e4qciA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A	V-set_3	e4qciA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
F [auth L]	C1-set_1	e4qciL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F [auth L]	V-set_3	e4qciL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
B	V-set_8	e4qciB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B	C1-set_1	e4qciB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth H]	V-set_8	e4qciH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth H]	C1-set_1	e4qciH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C	PDGF	e4qciC1	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	PDGF	e4qciD1	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)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	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)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
D	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, F [auth L]	Light Chain	IGLV3	Lambda	platelet-derived growth factor subunit b	SAbDab (2024-04-19)
B, E [auth H]	Heavy Chain	IGHV3	-	platelet-derived growth factor subunit b	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF04692	Platelet-derived growth factor, N terminal region (PDGF_N)	Platelet-derived growth factor, N terminal region	-	Family
C, D	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, F [auth L]	anti-PDGF-BB antibody - Light Chain	-	-	-
B, E [auth H]	anti-PDGF-BB antibody - Heavy chain	-	-	-
C, D	Platelet-derived growth factor subunit B	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 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 protein binding regulation of molecular function negative regulation of protein binding negative regulation of binding regulation of binding 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 protein binding regulation of molecular function negative regulation of protein binding negative regulation of binding regulation of binding biological regulation negative regulation of molecular function regulation of biological process regulation of cellular process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion positive regulation of biological process cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion cellular process positive regulation of cellular process cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic 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 regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process regulation of miRNA metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process miRNA transcription regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process ncRNA metabolic process 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 connective tissue development cellular developmental process metanephric glomerulus development metanephric glomerular mesangial cell development mesangial cell development cell development epithelial cell differentiation kidney vasculature development renal system vasculature development pericyte cell differentiation mesangial cell differentiation cell differentiation nephron development metanephric nephron development blood vessel development epithelial cell differentiation involved in kidney development epithelium development metanephric mesangial cell differentiation glomerular mesangium development tissue development cell differentiation involved in metanephros development vasculature development glomerular mesangial cell development glomerular mesangial cell differentiation metanephric glomerular mesangium development glomerulus 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 regulation of body fluid levels renal system process system process regulation of renal system process regulation of blood pressure regulation of system process regulation of glomerular filtration positive regulation of glomerular filtration regulation of systemic arterial blood pressure circulatory system process renal system process involved in regulation of blood volume positive regulation of multicellular organismal process regulation of multicellular organismal process renal system process involved in regulation of systemic arterial blood pressure regulation of biological quality glomerular filtration renal filtration blood circulation protein phosphorylation organonitrogen compound metabolic process 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 negative regulation of biological process negative regulation of lipid biosynthetic process negative regulation of cellular metabolic process regulation of phosphate metabolic process regulation of phosphatidylinositol biosynthetic process negative regulation of phosphatidylinositol biosynthetic process negative regulation of metabolic process negative regulation of cellular biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process regulation of phospholipid biosynthetic process glycerolipid biosynthetic process organophosphate biosynthetic process cellular lipid metabolic process glycerolipid metabolic process regulation of phosphorus metabolic process negative regulation of lipid metabolic process glycerophospholipid metabolic process lipid biosynthetic process negative regulation of phosphate metabolic process phospholipid metabolic process negative regulation of cellular process negative regulation of phospholipid biosynthetic process phosphatidylinositol metabolic process glycerophospholipid biosynthetic process regulation of phospholipid metabolic process negative regulation of phospholipid metabolic process negative regulation of biosynthetic process organophosphate metabolic process negative regulation of phosphorus metabolic process regulation of lipid biosynthetic process lipid metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process 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 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 organonitrogen compound biosynthetic process carbohydrate derivative metabolic process positive regulation of hyaluronan biosynthetic process glycosaminoglycan biosynthetic process carbohydrate biosynthetic process hyaluronan biosynthetic process positive regulation of carbohydrate metabolic process mucopolysaccharide metabolic process glycosaminoglycan metabolic process regulation of hyaluronan biosynthetic process regulation of polysaccharide metabolic process hyaluronan metabolic process polysaccharide metabolic process regulation of carbohydrate metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process regulation of polysaccharide biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic 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 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 regulation of 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 epithelial cell migration tissue migration ameboidal-type cell migration blood vessel endothelial cell migration regulation of endothelial cell migration epithelial cell migration regulation of epithelial cell migration positive regulation of blood vessel endothelial cell migration epithelium migration positive 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 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 transferase 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 organic substance cellular response to organic cyclic compound response to oxygen-containing compound cellular response to mycophenolic acid cellular response to oxygen-containing compound response to mycophenolic acid cellular response to organic substance response to organic cyclic 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 protein kinase C signaling 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 cellular response to cytokine stimulus protein autophosphorylation regulation of protein autophosphorylation positive regulation of protein autophosphorylation positive regulation of peptidyl-tyrosine phosphorylation regulation of peptidyl-tyrosine phosphorylation	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity 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 cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity 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 Golgi lumen

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P01127	dermatofibrosarcoma protuberans basal ganglia calcification, idiopathic, 5 familial meningioma essential thrombocythemia basal ganglia calcification, idiopathic, 1 pulmonary fibrosis bilateral striopallidodentate calcinosis Fibrosis retinal disease calcinosis 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 pulmonary fibrosis bilateral striopallidodentate calcinosis Fibrosis retinal disease calcinosis 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 rheumatoid arthritis cancer fibrosarcoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.