2QQK | pdb_00002qqk

Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth H]	d2qqkh1	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 [auth L]	d2qqkl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d2qqkl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	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)
A	SCOP2B Superfamily	galactose-binding domain-like	8069035	3000087	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	F5_F8_type_C	e2qqkA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: F5_F8_type_C	ECOD (1.6)
A	CUB	e2qqkA3	A: beta sandwiches	X: jelly-roll	H: Spermadhesin, CUB domain (From Topology)	T: Spermadhesin, CUB domain	F: CUB	ECOD (1.6)
B [auth H]	V-set_8	e2qqkH1	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 [auth H]	C1-set_1	e2qqkH2	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 [auth L]	C1-set_4	e2qqkL2	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 [auth L]	V-set	e2qqkL1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [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
B [auth H]	Semaphorin-Blocking Fab	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202514-0)
C [auth L]	Semaphorin-Blocking Fab	L-KAPPA	Homo sapiens (human)	IGKV1D-1301, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202514-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV3	-	neuropilin-2	SAbDab (2025-04-18)
C [auth L]	Light Chain	IGKV1D	Kappa	neuropilin-2	SAbDab (2025-04-18)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00754	F5/8 type C domain (F5_F8_type_C)	F5/8 type C domain	This domain is also known as the discoidin (DS) domain family [1].	Domain
A	PF00431	CUB domain (CUB)	CUB domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Neuropilin-2	cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity semaphorin receptor activity growth factor binding cytokine binding catalytic activity, acting on a protein cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity semaphorin receptor activity growth factor binding cytokine binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups vascular endothelial growth factor receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity catalytic activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process multicellular organismal process cranial ganglion development nervous system development tissue development ganglion development multicellular organism development nerve development cranial nerve development facioacoustic ganglion development anatomical structure development system development cellular developmental process cell projection organization developmental process multicellular organismal process cranial ganglion development nervous system development tissue development ganglion development multicellular organism development nerve development cranial nerve development facioacoustic ganglion development anatomical structure development system development cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis sympathetic neuron projection guidance neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development cellular process blastoderm segmentation segmentation neural crest cell development pattern specification process mesenchyme development embryo development mesenchymal cell migration ameboidal-type cell migration cell migration cell motility neural crest cell migration stem cell development neural crest cell differentiation ventral trunk neural crest cell migration embryonic pattern specification animal organ development regionalization trunk neural crest cell migration stem cell differentiation mesenchymal cell differentiation trunk segmentation axonogenesis motor neuron axon guidance branchiomotor neuron axon guidance axon guidance axon development cell morphogenesis involved in neuron differentiation heart development cardiac chamber morphogenesis heart morphogenesis circulatory system development cardiac septum development cardiac septum morphogenesis cardiac chamber development outflow tract septum morphogenesis outflow tract morphogenesis animal organ morphogenesis gonadotrophin-releasing hormone neuronal migration to the hypothalamus hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development neuron migration forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development central nervous system development hypothalamic tangential migration using cell-axon interactions forebrain neuron differentiation hypothalamus cell migration chemotaxis negative chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion cell adhesion sensory neuron axon guidance regulation of biological process regulation of cellular component organization regulation of cellular process postsynapse organization biological regulation regulation of postsynapse organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality cranial nerve morphogenesis vestibulocochlear nerve structural organization cranial nerve structural organization vestibulocochlear nerve development vestibulocochlear nerve morphogenesis anatomical structure arrangement parasympathetic nervous system development preganglionic parasympathetic fiber development facial nerve morphogenesis autonomic nervous system development facial nerve structural organization facial nerve development positive regulation of locomotion regulation of cell motility endothelial cell migration positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration positive regulation of cellular process blood vessel morphogenesis tube development angiogenesis vasculature development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development neural crest cell migration involved in autonomic nervous system development axon extension developmental growth cell growth axon extension involved in axon guidance neuron projection extension involved in neuron projection guidance neuron projection extension developmental cell growth growth developmental growth involved in morphogenesis sympathetic nervous system development sympathetic ganglion development sympathetic neuron projection extension trigeminal nerve development trigeminal nerve structural organization trigeminal nerve morphogenesis cellular response to stimulus cell surface receptor signaling pathway semaphorin-plexin signaling pathway signaling cell communication signal transduction ganglion morphogenesis dorsal root ganglion morphogenesis tissue morphogenesis dorsal root ganglion development 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 trigeminal ganglion development response to peptide response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor	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 receptor complex glutamatergic synapse 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 receptor complex glutamatergic synapse axon cell projection neuron projection plasma membrane bounded cell projection extracellular region
B [auth H]	Antibody Heavy Chain	-	-	-
C [auth L]	Antibody Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR014648	Neuropilin	Family
A	IPR050633	Neuropilin/Multicopper Oxidase/Coagulation Factor	Family
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR000998	MAM domain	Domain
A	IPR000859	CUB domain	Domain
A	IPR022579	Neuropilin, C-terminal	Domain
A	IPR000421	Coagulation factor 5/8, C-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O60462	visual epilepsy interstitial cystitis tuberculosis large cell medulloblastoma malignant colon neoplasm malignant mesothelioma Myoclonic Seizures astrocytic tumor ovarian cancer autism primitive neuroectodermal tumor cystic fibrosis gastric carcinoma glioblastoma invasive ductal breast carcinoma visual epilepsy interstitial cystitis tuberculosis large cell medulloblastoma malignant colon neoplasm malignant mesothelioma Myoclonic Seizures astrocytic tumor ovarian cancer autism primitive neuroectodermal tumor cystic fibrosis gastric carcinoma glioblastoma invasive ductal breast carcinoma lung cancer malignant ependymoma malignant pancreatic neoplasm adenoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm lung carcinoma malignant glioma MALT lymphoma adrenal cortex carcinoma osteosarcoma atypical teratoid rhabdoid tumor pilocytic astrocytoma breast cancer subependymal giant cell astrocytoma

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.