3QWN

Crystal structure of a NigD-like immunity protein (BACCAC_03262) from Bacteroides caccae ATCC 43185 at 2.42 A resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2 Family	NTD of NigD-like	8047775	4005812	SCOP2 (2022-06-29)
H	SCOP2 Family	CTD of NigD-like	8046949	4005383	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	Bacterial enterotoxins	8052332	3000434	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	CTD of NigD-like	8052333	3002106	SCOP2 (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	PF12667	e3qwnA4	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
A	PF17415	e3qwnA3	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
B	PF12667	e3qwnB2	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
B	PF17415	e3qwnB1	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
C	PF12667	e3qwnC4	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
C	PF17415	e3qwnC3	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
D	PF12667	e3qwnD4	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
D	PF17415	e3qwnD3	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
E	PF12667	e3qwnE4	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
E	PF17415	e3qwnE3	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
F	PF12667	e3qwnF4	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
F	PF17415	e3qwnF3	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
G	PF12667	e3qwnG2	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
G	PF17415	e3qwnG1	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
H	PF12667	e3qwnH2	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
H	PF17415	e3qwnH1	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
I	PF12667	e3qwnI4	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
I	PF17415	e3qwnI3	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
J	PF12667	e3qwnJ2	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
J	PF17415	e3qwnJ1	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
K	PF12667	e3qwnK4	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
K	PF17415	e3qwnK3	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)
L	PF12667	e3qwnL4	A: beta barrels	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins (From Topology)	T: OB domain in putative lipoprotein BF3042-related proteins	F: PF12667	ECOD (1.6)
L	PF17415	e3qwnL3	A: beta sandwiches	X: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	H: Ig-like domain in putative lipoprotein BF3042-related proteins (From Topology)	T: Ig-like domain in putative lipoprotein BF3042-related proteins	F: PF17415	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
A	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
B	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
B	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
C	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
C	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
D	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
D	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
E	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
E	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
F	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
F	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
G	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
G	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
H	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
H	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
I	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
I	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
J	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
J	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
K	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
K	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)
L	2.40.50.500	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	NigD-like N-terminal OB domain	CATH (4.3.0)
L	2.60.40.2370	Mainly Beta	Sandwich	Immunoglobulin-like	NigD-like, C-terminal beta sandwich domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF17415	NigD-like C-terminal beta sandwich domain (NigD_C)	NigD-like C-terminal beta sandwich domain	This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attach ...	This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attachment site. The family includes NigD a protein found in the Nig operon that encodes a bacteriocin called nigrescin. It has been suggested that NigD may be the immunity protein for nigrescin (NigC) because it is directly downstream [1]. This entry represents the C-terminal beta-sandwich domain of NigD.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF12667	NigD-like N-terminal OB domain (NigD_N)	NigD-like N-terminal OB domain	This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attach ...	This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attachment site. The family includes NigD a protein found in the Nig operon that encodes a bacteriocin called nigrescin. It has been suggested that NigD may be the immunity protein for nigrescin (NigC) because it is directly downstream [1]. This domain has an OB fold.	Domain

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.

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3QWN

Crystal structure of a NigD-like immunity protein (BACCAC_03262) from Bacteroides caccae ATCC 43185 at 2.42 A resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage