8BF4 | pdb_00008bf4

Crystal structure of Mouse Plexin-B1 (20-535) in complex with VHH15 and VHH14

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth A]	3HCDH_N	e8bf4A1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: 3HCDH_N	ECOD (v294.1)
A [auth D]	3HCDH_N	e8bf4D1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: 3HCDH_N	ECOD (v294.1)
E [auth C]	3HCDH_N	e8bf4C1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: 3HCDH_N	ECOD (v294.1)
B [auth F]	3HCDH_N	e8bf4F1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: 3HCDH_N	ECOD (v294.1)
F [auth B]	3HCDH_N	e8bf4B1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: 3HCDH_N	ECOD (v294.1)
C [auth E]	3HCDH_N	e8bf4E1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: 3HCDH_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth D], D [auth A]	Heavy Chain	IGHV1	-	plexin-b1	SAbDab (2026-04-10)
C [auth E], F [auth B]	Heavy Chain	IGHV1	-	plexin-b1	SAbDab (2026-04-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth F], E [auth C]	PF01437	Plexin repeat (PSI)	Plexin repeat	-	Family
B [auth F], E [auth C]	PF01403	Sema domain (Sema)	Sema domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], D [auth A]	VHH14	-	-	-
B [auth F], E [auth C]	Plexin-B1	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity GTPase activating protein binding protein binding binding	positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity multicellular organismal process positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity multicellular organismal process positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process regulation of biological process regulation of cell projection organization positive regulation of cell development nervous system development generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell morphogenesis cellular component organization regulation of nervous system development neurogenesis positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis positive regulation of axonogenesis regulation of anatomical structure morphogenesis positive regulation of cellular process regulation of multicellular organismal development plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development cellular process regulation of plasma membrane bounded cell projection organization cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction Rho protein signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of 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 regulation of cytoskeleton organization regulation of organelle organization organelle organization cytoskeleton organization regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion regulation of cell shape regulation of cell morphogenesis regulation of biological quality negative regulation of cell population proliferation cell population proliferation negative regulation of biological process osteoblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of osteoblast proliferation regulation of osteoblast proliferation cell surface receptor signaling pathway semaphorin-plexin signaling pathway bone maturation animal organ development developmental maturation skeletal system development ossification anatomical structure maturation ossification involved in bone maturation animal organ maturation bone development inhibitory synapse assembly cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization synapse assembly cell adhesion regulation of cell adhesion negative regulation of cell adhesion	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane protein-containing complex semaphorin receptor complex signaling receptor complex glutamatergic synapse
C [auth E], F [auth B]	VHH15	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth F], E [auth C]	IPR002909	IPT domain	Domain
B [auth F], E [auth C]	IPR041362	Plexin, TIG domain 2	Domain
B [auth F], E [auth C]	IPR016201	PSI domain	Domain
B [auth F], E [auth C]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B [auth F], E [auth C]	IPR008936	Rho GTPase activation protein	Homologous Superfamily
B [auth F], E [auth C]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B [auth F], E [auth C]	IPR002165	Plexin repeat	Repeat
B [auth F], E [auth C]	IPR057533	Plexin-B, PSI domain	Domain
B [auth F], E [auth C]	IPR041019	Plexin, TIG domain 1	Domain
B [auth F], E [auth C]	IPR031148	Plexin family	Family
B [auth F], E [auth C]	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
B [auth F], E [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth F], E [auth C]	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
B [auth F], E [auth C]	IPR036352	Sema domain superfamily	Homologous Superfamily
B [auth F], E [auth C]	IPR001627	Sema domain	Domain

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.