5O1R

human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B

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

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth L]	d5o1rl2	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)
E [auth L]	d5o1rl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth M]	d5o1rm2	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)
F [auth M]	d5o1rm1	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	TbpB N-lobe and C-lobe beta-barrel domains-like	8052230	3002098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8052230	3002098	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	TbpB_B_D	e5o1rA1	A: beta barrels	X: Outer membrane meander beta-barrels	H: OMPA-like (From Topology)	T: OMPA-like	F: TbpB_B_D	ECOD (1.6)
B	TbpB_B_D	e5o1rB1	A: beta barrels	X: Outer membrane meander beta-barrels	H: OMPA-like (From Topology)	T: OMPA-like	F: TbpB_B_D	ECOD (1.6)
D [auth I]	V-set_8	e5o1rI1	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 I]	C1-set_1	e5o1rI2	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 H]	V-set_8	e5o1rH2	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)
C [auth H]	C1-set_1	e5o1rH1	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)
E [auth L]	C1-set_4	e5o1rL2	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 L]	V-set	e5o1rL1	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)
F [auth M]	C1-set_4	e5o1rM1	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)
F [auth M]	V-set	e5o1rM2	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	2.40.160.90	Mainly Beta	Beta Barrel	Porin		CATH (utative)
B	2.40.160.90	Mainly Beta	Beta Barrel	Porin		CATH (utative)
D [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth M]	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 [auth H], D [auth I]	Fab 5H2	VH-CH1	Homo sapiens (human)	IGHV4-6101, IGHJ401, IGHJ501, IGHJ502, IGHJ402, IGHJ403, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
E [auth L], F [auth M]	Fab 5H2	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ201, IGKJ202, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], D [auth I]	Heavy Chain	IGHV4	-	gna2132	SAbDab (2024-04-19)
E [auth L], F [auth M]	Light Chain	IGKV1	Kappa	gna2132	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01298	C-lobe and N-lobe beta barrels of Tf-binding protein B (TbpB_B_D)	C-lobe and N-lobe beta barrels of Tf-binding protein B	Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis ...	Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a "handle" domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. This domain family is found in C and N lobe eight stranded beta barrel region of TbpB proteins. The eight-stranded barrel domains in N and C lobe draw comparisons to eight-stranded beta barrel outer-membrane protein W (OmpW). However, the barrel domains of TbpB have the hydrophobic residues line the inner surface of the beta barrels to create a stable hydrophobic core [2].	Domain
C [auth H], D [auth I]	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 [auth H], D [auth I]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
E [auth L], F [auth M]	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
E [auth L], F [auth M]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	GNA2132	DNA binding binding organic cyclic compound binding nucleic acid binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	cell adhesion cellular process	cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane cellular anatomical entity
C [auth H], D [auth I]	IGH@ protein	-	-	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex
E [auth L], F [auth M]	Uncharacterized protein	-	-	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
A, B	IPR001677	Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain	Domain
C [auth H], D [auth I]	IPR003597	Immunoglobulin C1-set	Domain
C [auth H], D [auth I]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth H], D [auth I]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H], D [auth I]	IPR003599	Immunoglobulin subtype	Domain
C [auth H], D [auth I]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth H], D [auth I]	IPR007110	Immunoglobulin-like domain	Domain
C [auth H], D [auth I]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
E [auth L], F [auth M]	IPR003597	Immunoglobulin C1-set	Domain
E [auth L], F [auth M]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth L], F [auth M]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth L], F [auth M]	IPR003599	Immunoglobulin subtype	Domain
E [auth L], F [auth M]	IPR013106	Immunoglobulin V-set domain	Domain
E [auth L], F [auth M]	IPR007110	Immunoglobulin-like domain	Domain
E [auth L], F [auth M]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.