4C2D | pdb_00004c2d

Crystal structure of the protease CtpB in an active state

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PDZ_2	e4c2dA5	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ_2	ECOD (1.6)
A	PG_binding_1	e4c2dA2	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: PG_binding_1	ECOD (1.6)
A	Peptidase_S41_CPP	e4c2dA6	A: alpha bundles	X: Tail specific protease helical domain (From Topology)	H: Tail specific protease helical domain (From Topology)	T: Tail specific protease helical domain	F: Peptidase_S41_CPP	ECOD (1.6)
A	Peptidase_S41	e4c2dA4	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Peptidase_S41	ECOD (1.6)
B	PDZ_2	e4c2dB5	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ_2	ECOD (1.6)
B	PG_binding_1	e4c2dB2	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: PG_binding_1	ECOD (1.6)
B	Peptidase_S41_CPP	e4c2dB6	A: alpha bundles	X: Tail specific protease helical domain (From Topology)	H: Tail specific protease helical domain (From Topology)	T: Tail specific protease helical domain	F: Peptidase_S41_CPP	ECOD (1.6)
B	Peptidase_S41	e4c2dB4	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Peptidase_S41	ECOD (1.6)
C	PDZ_2	e4c2dC5	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ_2	ECOD (1.6)
C	PG_binding_1	e4c2dC2	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: PG_binding_1	ECOD (1.6)
C	Peptidase_S41_CPP	e4c2dC6	A: alpha bundles	X: Tail specific protease helical domain (From Topology)	H: Tail specific protease helical domain (From Topology)	T: Tail specific protease helical domain	F: Peptidase_S41_CPP	ECOD (1.6)
C	Peptidase_S41	e4c2dC4	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Peptidase_S41	ECOD (1.6)
D	PG_binding_1	e4c2dD2	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: PG_binding_1	ECOD (1.6)
D	Peptidase_S41_CPP	e4c2dD3	A: alpha bundles	X: Tail specific protease helical domain (From Topology)	H: Tail specific protease helical domain (From Topology)	T: Tail specific protease helical domain	F: Peptidase_S41_CPP	ECOD (1.6)
D	Peptidase_S41	e4c2dD1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Peptidase_S41	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (utative)
A	1.10.101.10	Mainly Alpha	Orthogonal Bundle	Muramoyl-pentapeptide Carboxypeptidase	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13180	PDZ domain (PDZ_2)	PDZ domain		Domain
A, B, C, D	PF03572	Peptidase family S41 (Peptidase_S41)	Peptidase family S41	-	Family
A, B, C, D	PF01471	Putative peptidoglycan binding domain (PG_binding_1)	Putative peptidoglycan binding domain	This domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is ...	This domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins [3]. The domain is found to bind peptidoglycan experimentally [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	CARBOXY-TERMINAL PROCESSING PROTEASE CTPB	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity peptide binding	metabolic process cellular process peptide metabolic process sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation proteolysis primary metabolic process protein metabolic process macromolecule metabolic process cellular response to stimulus metabolic process cellular process peptide metabolic process sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation proteolysis primary metabolic process protein metabolic process macromolecule metabolic process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction cell communication	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space
E, F, G, H	PEPTIDE1	-	-	-
I [auth M]	PEPTIDE2	-	-	-
J [auth N], K [auth O], L [auth P]	PEPTIDE2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002477	Peptidoglycan binding-like	Domain
A, B, C, D	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR036034	PDZ superfamily	Homologous Superfamily
A, B, C, D	IPR036365	PGBD-like superfamily	Homologous Superfamily
A, B, C, D	IPR005151	Tail specific protease	Domain
A, B, C, D	IPR001478	PDZ domain	Domain
A, B, C, D	IPR004447	C-terminal-processing peptidase S41A	Family
A, B, C, D	IPR055210	Activating protease CtpA/B, N-terminal domain	Domain
A, B, C, D	IPR036366	PGBD superfamily	Homologous Superfamily

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.