2J9P

Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d2j9pb1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	Penicillin-binding protein DacC	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
A	d2j9pa1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	Penicillin-binding protein DacC	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032880	3001604	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032880	3001604	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)
B	PF02113	e2j9pB1	A: beta complex topology	X: Inserted beta sandwich domain in Dac-like proteins (From Topology)	H: Inserted beta sandwich domain in Dac-like proteins (From Topology)	T: Inserted beta sandwich domain in Dac-like proteins	F: PF02113	ECOD (1.6)
B	PF02113	e2j9pB2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: PF02113	ECOD (1.6)
B	PF02113	e2j9pB3	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: PF02113	ECOD (1.6)
B	PF02113	e2j9pB4	A: a/b three-layered sandwiches	X: DTD-like	H: Inserted a+b domain in Dac-like proteins (From Topology)	T: Inserted a+b domain in Dac-like proteins	F: PF02113	ECOD (1.6)
A	PF02113	e2j9pA1	A: beta complex topology	X: Inserted beta sandwich domain in Dac-like proteins (From Topology)	H: Inserted beta sandwich domain in Dac-like proteins (From Topology)	T: Inserted beta sandwich domain in Dac-like proteins	F: PF02113	ECOD (1.6)
A	PF02113	e2j9pA2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: PF02113	ECOD (1.6)
A	PF02113	e2j9pA3	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: PF02113	ECOD (1.6)
A	PF02113	e2j9pA4	A: a/b three-layered sandwiches	X: DTD-like	H: Inserted a+b domain in Dac-like proteins (From Topology)	T: Inserted a+b domain in Dac-like proteins	F: PF02113	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
B	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
A	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02113	D-Ala-D-Ala carboxypeptidase 3 (S13) family (Peptidase_S13)	D-Ala-D-Ala carboxypeptidase 3 (S13) family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	D-alanyl-D-alanine carboxypeptidase DacC	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type carboxypeptidase activity serine-type peptidase activity hydrolase activity exopeptidase activity catalytic activity carboxypeptidase activity serine-type D-Ala-D-Ala carboxypeptidase activity	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular process cell cycle organic substance metabolic process developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular process cell cycle organic substance metabolic process organonitrogen compound metabolic process glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process carbohydrate derivative metabolic process metabolic process macromolecule metabolic process cell division cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization cellular biosynthetic process organonitrogen compound biosynthetic process cellular component biogenesis organic substance biosynthetic process glycosaminoglycan biosynthetic process carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cellular metabolic process macromolecule biosynthetic process peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan biosynthetic process proteolysis primary metabolic process protein metabolic process	extracellular region cellular anatomical entity membrane microdomain membrane raft membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C	Family

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.