2YPV | pdb_00002ypv

Crystal structure of the Meningococcal vaccine antigen factor H binding protein in complex with a bactericidal antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth L]	d2ypvl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d2ypvl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d2ypvh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d2ypvh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth L]		e2ypvL1	A: Alpha-beta plaits	X: Family B DNA polymerase insertion domain	H: Family B DNA polymerase insertion domain	T: Beta-lactamase2	F:	ECOD (20:10:01)
B [auth H]		e2ypvH1	A: Alpha-beta plaits	X: Family B DNA polymerase insertion domain	H: Family B DNA polymerase insertion domain	T: Beta-lactamase2	F:	ECOD (20:10:01)
A		e2ypvA1	A: Alpha-beta plaits	X: Pseudouridine synthase	H: Pseudouridine synthase	T: MG2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.1980	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.40.160.90	Mainly Beta	Beta Barrel	Porin		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 [auth L]	Fab 12C1	L-KAPPA	Mus musculus (house mouse)	IGKV14-11101, IGKJ101, IGKJ102, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202609-0)
B [auth H]	Fab 12C1	VH-CH1	Mus musculus (house mouse)	IGHV1-3901, IGHJ201, IGHG2B*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L]	Light Chain	IGKV14	Kappa	lipoprotein	SAbDab (2026-03-13)
B [auth H]	Heavy Chain	IGHV1	-	lipoprotein	SAbDab (2026-03-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08794	Factor H binding protein, C-terminal (FHBP_C)	Factor H binding protein, C-terminal	Factor H binding protein (also known as GNA1870) is a surface exposed lipoprotein in Neisseria meningitidis that is a potent antigen and a potential candidate for a vaccine against meningococcal disease [1-4]. The structure of the C-terminal domain c ...	Factor H binding protein (also known as GNA1870) is a surface exposed lipoprotein in Neisseria meningitidis that is a potent antigen and a potential candidate for a vaccine against meningococcal disease [1-4]. The structure of the C-terminal domain consists of an anti-parallel beta barrel overlaid by a short alpha helical region [1,5]. This domain is highly similar to Transferrin-binding protein B beta barrel (Pfam:PF01298).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth L]	FAB 12C1	-	-	-
B [auth H]	FAB 12C1	-	-	-
A	LIPOPROTEIN	-	-	membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle bacterial extracellular vesicle vesicle extracellular membrane-bounded organelle cell periphery cell outer membrane external encapsulating structure membrane cell envelope membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle bacterial extracellular vesicle vesicle extracellular membrane-bounded organelle cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
A	IPR014902	Factor H binding protein-like, C-terminal	Domain
A	IPR049377	Factor H binding protein, N-terminal	Domain
A	IPR049378	Factor H binding protein	Family

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.