2VWE

Crystal Structure of Vascular Endothelial Growth Factor-B in Complex with a Neutralizing Antibody Fab Fragment

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
B	SCOP2B Superfamily	Cystine-knot cytokines	8070297	3000846	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cystine-knot cytokines	8070297	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)
B	PDGF	e2vweB1	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	e2vweA1	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	C1-set_4	e2vweC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
C	V-set	e2vweC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E [auth J]	C1-set_4	e2vweJ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E [auth J]	V-set	e2vweJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D [auth E]	V-set_8	e2vweE1	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)
D [auth E]	C1-set_1	e2vweE2	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_8	e2vweL1	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)
F [auth L]	C1-set_1	e2vweL2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth E]	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)

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
C, E [auth J]	Anti-VEGF-B monoclonal antibody	L-KAPPA	Mus musculus (house mouse)	IGKV10-9601, IGKV10-9602, IGKJ102, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2C_KAPPA	IMGT (202449-0)
D [auth E], F [auth L]	Anti-VEGF-B monoclonal antibody	VH-CH1	Mus musculus (house mouse)	IGHV1-5301, IGHJ401, IGHG2C01, IGHG2C02, IGHG2C*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2C_KAPPA	IMGT (202449-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, E [auth J]	Light Chain	IGKV10	Kappa	vascular endothelial growth factor b	SAbDab (2024-12-13)
D [auth E], F [auth L]	Heavy Chain	IGHV1	-	vascular endothelial growth factor b	SAbDab (2024-12-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	VASCULAR ENDOTHELIAL GROWTH FACTOR 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 vascular endothelial growth factor receptor 1 binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding chemoattractant activity 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 vascular endothelial growth factor receptor 1 binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding chemoattractant activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding	positive chemotaxis chemotaxis positive regulation of locomotion regulation of biological process response to stimulus regulation of response to external stimulus positive regulation of positive chemotaxis biological regulation positive regulation of biological process response to external stimulus induction of positive chemotaxis regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus regulation of positive chemotaxis positive chemotaxis chemotaxis positive regulation of locomotion regulation of biological process response to stimulus regulation of response to external stimulus positive regulation of positive chemotaxis biological regulation positive regulation of biological process response to external stimulus induction 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 response to chemical regulation of locomotion locomotion cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication cellular process ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway positive regulation of vascular endothelial growth factor receptor signaling pathway response to growth factor vascular endothelial growth factor signaling pathway cellular response to vascular endothelial growth factor stimulus regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration myeloid leukocyte migration cell migration regulation of immune system process cell motility positive regulation of immune system process regulation of mast cell chemotaxis cell chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration mast cell migration positive regulation of leukocyte chemotaxis positive regulation of leukocyte migration leukocyte migration positive regulation of mast cell chemotaxis cellular response to chemical stimulus immune system process mast cell chemotaxis leukocyte chemotaxis 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 developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis sprouting angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process positive regulation of cell division cell division regulation of cell division regulation of developmental process regulation of vasculature development regulation of response to wounding positive regulation of developmental process positive regulation of vascular wound healing vascular wound healing response to stress regulation of response to stress regulation of multicellular organismal process response to wounding regulation of anatomical structure morphogenesis positive regulation of response to wounding wound healing regulation of multicellular organismal development angiogenesis involved in wound healing positive regulation of angiogenesis positive regulation of vasculature development positive regulation of wound healing regulation of angiogenesis regulation of wound healing positive regulation of multicellular organismal process regulation of vascular wound healing response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus heart process system process circulatory system process cardiac muscle contraction heart contraction muscle contraction muscle system process blood circulation striated muscle contraction regulation of biosynthetic process negative regulation of metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation heart development animal organ development coronary vasculature development carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein glycosylation glycosylation macromolecule modification macromolecule glycosylation protein O-linked glycosylation protein metabolic process protein modification process regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process peptidyl-tyrosine modification positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation	cellular anatomical structure membrane extracellular region membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure membrane extracellular region membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen organelle secretory granule secretory vesicle cytoplasm platelet alpha granule vesicle platelet alpha granule lumen extracellular space
C, E [auth J]	ANTI-VEGF-B MONOCLONAL ANTIBODY	-	-	-
D [auth E], F [auth L]	ANTI-VEGF-B MONOCLONAL ANTIBODY	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B	IPR023581	Platelet-derived growth factor, conserved site	Conserved Site
A, B	IPR000072	PDGF/VEGF domain	Domain
A, B	IPR050507	Platelet-derived/Vascular endothelial growth factor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P49765	psoriasis breast carcinoma Mammary Neoplasms, Human pancreatic neoplasm wet macular degeneration alopecia areata breast cancer glioblastoma malignant mesothelioma malignant pancreatic neoplasm attention deficit hyperactivity disorder, inattentive type Crohn disease hypertensive disorder neovascular glaucoma vitiligo psoriasis breast carcinoma Mammary Neoplasms, Human pancreatic neoplasm wet macular degeneration alopecia areata breast cancer glioblastoma malignant mesothelioma malignant pancreatic neoplasm attention deficit hyperactivity disorder, inattentive type Crohn disease hypertensive disorder neovascular glaucoma vitiligo breast fibroadenoma diabetic macular edema ductal breast carcinoma in situ invasive ductal breast 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.