2VWE | pdb_00002vwe

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)
E [auth J]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091539	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091539	3000071	SCOP2B (2022-06-29)
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	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth L]	e2vweL1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
D [auth E]	e2vweE1	A: Profilin-like	X: sensor domains	H: sensor domains	T: PID	F:	ECOD (20:10:01)
E [auth J]	e2vweJ1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
C	e2vweC1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
B	e2vweB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
A	e2vweA1	A: Profilin-like	X: sensor domains	H: sensor domains	T: PID	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

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
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 (202609-0)
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 (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth E], F [auth L]	Heavy Chain	IGHV1	-	vascular endothelial growth factor b	SAbDab (2026-03-13)
C, E [auth J]	Light Chain	IGKV10	Kappa	vascular endothelial growth factor b	SAbDab (2026-03-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth E], F [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
C, E [auth J]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C, E [auth J]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
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
D [auth E], F [auth L]	ANTI-VEGF-B MONOCLONAL ANTIBODY	protein binding binding signaling receptor binding immunoglobulin receptor binding antigen binding	humoral immune response biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response immune response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress immune system process humoral immune response biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response immune response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress immune system process response to bacterium response to external biotic stimulus adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process biological regulation immunoglobulin mediated immune response adaptive immune response immune effector process regulation of response to stimulus B cell mediated immunity regulation of immune response activation of immune response	protein-containing complex cellular anatomical structure extracellular region extracellular space immunoglobulin complex, circulating immunoglobulin complex
C, E [auth J]	ANTI-VEGF-B MONOCLONAL ANTIBODY	-	response to stimulus immune response immune system process adaptive immune response developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation response to stimulus immune response immune system process adaptive immune response developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation anatomical structure development cellular process leukocyte differentiation	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region plasma membrane protein complex membrane protein complex alpha-beta T cell receptor complex receptor complex plasma membrane signaling receptor complex T cell receptor complex IgG immunoglobulin complex
A, B	VASCULAR ENDOTHELIAL GROWTH FACTOR B	molecular function activator activity 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 protein binding binding signaling receptor binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding chemoattractant activity molecular function activator activity 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 protein binding binding signaling receptor 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 anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development 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 cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation 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 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 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 O-linked glycosylation protein metabolic 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 peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein modification 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 macromolecule modification 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E], F [auth L]	IPR003597	Immunoglobulin C1-set	Domain
D [auth E], F [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth E], F [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth E], F [auth L]	IPR007110	Immunoglobulin-like domain	Domain
D [auth E], F [auth L]	IPR050380	Immune Recognition and Response Modulators	Family
D [auth E], F [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C, E [auth J]	IPR050150	Immunoglobulin Variable Light Chain	Family
C, E [auth J]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, E [auth J]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, E [auth J]	IPR013106	Immunoglobulin V-set domain	Domain
C, E [auth J]	IPR003599	Immunoglobulin domain subtype	Domain
C, E [auth J]	IPR007110	Immunoglobulin-like domain	Domain
C, E [auth J]	IPR003597	Immunoglobulin C1-set	Domain
C, E [auth J]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, E [auth J]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, E [auth J]	IPR007110	Immunoglobulin-like domain	Domain
C, E [auth J]	IPR050380	Immune Recognition and Response Modulators	Family
C, E [auth J]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
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