3ZCZ

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor

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)
A	d3zcza_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	D-alanyl-D-alanine carboxypeptidase Dac	(Actinomadura sp. R39 ) [TaxId: 72570 ],	SCOPe (2.08)
B	d3zczb_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	D-alanyl-D-alanine carboxypeptidase Dac	(Actinomadura sp. R39 ) [TaxId: 72570 ],	SCOPe (2.08)
C	d3zczc_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	D-alanyl-D-alanine carboxypeptidase Dac	(Actinomadura sp. R39 ) [TaxId: 72570 ],	SCOPe (2.08)
D	d3zczd_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	D-alanyl-D-alanine carboxypeptidase Dac	(Actinomadura sp. R39 ) [TaxId: 72570 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032917	3001604	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032917	3001604	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032917	3001604	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032917	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)
A	PF02113	e3zczA1	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	e3zczA2	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	e3zczA3	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	e3zczA4	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)
B	PF02113	e3zczB1	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	e3zczB2	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	e3zczB3	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	e3zczB4	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)
C	PF02113	e3zczC1	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)
C	PF02113	e3zczC2	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)
C	PF02113	e3zczC3	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)
C	PF02113	e3zczC4	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)
D	PF02113	e3zczD1	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)
D	PF02113	e3zczD2	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)
D	PF02113	e3zczD3	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)
D	PF02113	e3zczD4	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)
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)
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)
C	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
C	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
D	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
D	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, C, D	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, C, D	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity 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 biosynthetic process cell wall organization or biogenesis glycosaminoglycan 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 biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process cellular component biogenesis organic substance metabolic process peptidoglycan metabolic process organic substance biosynthetic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis organonitrogen compound metabolic process cellular metabolic process macromolecule biosynthetic process peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process macromolecule metabolic process proteolysis primary metabolic process protein metabolic process cellular component organization cell wall organization external encapsulating structure organization response to stimulus response to chemical response to antibiotic	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C, D	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.