2VGJ

Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin

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	d2vgja_	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	d2vgjb_	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	d2vgjc_	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	d2vgjd_	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	Peptidase_S13_2nd	e2vgjA1	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: Peptidase_S13_2nd	ECOD (1.6)
A	Peptidase_S13_3rd	e2vgjA2	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: Peptidase_S13_3rd	ECOD (1.6)
A	Peptidase_S13_4th	e2vgjA3	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: Peptidase_S13_4th	ECOD (1.6)
A	Peptidase_S13_1st	e2vgjA4	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: Peptidase_S13_1st	ECOD (1.6)
B	Peptidase_S13_2nd	e2vgjB1	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: Peptidase_S13_2nd	ECOD (1.6)
B	Peptidase_S13_3rd	e2vgjB2	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: Peptidase_S13_3rd	ECOD (1.6)
B	Peptidase_S13_4th	e2vgjB3	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: Peptidase_S13_4th	ECOD (1.6)
B	Peptidase_S13_1st	e2vgjB4	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: Peptidase_S13_1st	ECOD (1.6)
C	Peptidase_S13_2nd	e2vgjC1	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: Peptidase_S13_2nd	ECOD (1.6)
C	Peptidase_S13_3rd	e2vgjC2	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: Peptidase_S13_3rd	ECOD (1.6)
C	Peptidase_S13_4th	e2vgjC3	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: Peptidase_S13_4th	ECOD (1.6)
C	Peptidase_S13_1st	e2vgjC4	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: Peptidase_S13_1st	ECOD (1.6)
D	Peptidase_S13_2nd	e2vgjD1	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: Peptidase_S13_2nd	ECOD (1.6)
D	Peptidase_S13_3rd	e2vgjD2	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: Peptidase_S13_3rd	ECOD (1.6)
D	Peptidase_S13_4th	e2vgjD3	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: Peptidase_S13_4th	ECOD (1.6)
D	Peptidase_S13_1st	e2vgjD4	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: Peptidase_S13_1st	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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis 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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis 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	cellular anatomical structure extracellular region

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 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.