Annotations: 4PQX

Crystal structure of a NigD-like protein (BACCAC_02139) from Bacteroides caccae ATCC 43185 at 2.39 A resolution

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	CTD of NigD-like	8046951	4005383	SCOP2 (2022-06-29)
A	SCOP2 Family	NTD of NigD-like	8047777	4005812	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CTD of NigD-like	8052340	3002106	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Bacterial enterotoxins	8052341	3000434	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)
D	zf-CCHC	e4pqxD1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: zf-CCHC	ECOD (v295.2)
C	zf-CCHC	e4pqxC1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: zf-CCHC	ECOD (v295.2)
B	zf-CCHC	e4pqxB1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: zf-CCHC	ECOD (v295.2)
A	zf-CCHC	e4pqxA1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: zf-CCHC	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR038143	NigD-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR038179	NigD-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR035376	NigD-like, C-terminal domain	Domain
A, B, C, D	IPR024299	NigD-like N-terminal OB domain	Domain

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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.