4OXD

Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	VanY	e4oxdA1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: VanY	ECOD (1.6)
B	VanY	e4oxdB1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: VanY	ECOD (1.6)
C	VanY	e4oxdC1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: VanY	ECOD (1.6)
D	VanY	e4oxdD1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: VanY	ECOD (1.6)
E	VanY	e4oxdE1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: VanY	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
B	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
C	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
D	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
E	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF02557	D-alanyl-D-alanine carboxypeptidase (VanY)	D-alanyl-D-alanine carboxypeptidase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	LdcB LD-carboxypeptidase	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	-
F [auth H]	MUB-ALA-ZGL-LYS-DSG	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR009045	Hedgehog signalling/DD-peptidase zinc-binding domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR052179	Bacterial Peptidoglycan Processing Enzymes	Family
A, B, C, D, E	IPR003709	Peptidase M15B	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
F [auth H]	DSG	RESID: AA0196 , AA0622 PSI-MOD : D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985
F [auth H]	ZGL	RESID: AA0196 , AA0622

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 R01GM133198.