4BXD

CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TETRASACCHARIDE PENTAPEPTIDE

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	UNK_F_TYPE	e4bxdA1	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: UNK_F_TYPE	ECOD (1.6)
A	Amidase_2	e4bxdA2	A: a+b three layers	X: N-acetylmuramoyl-L-alanine amidase-like (From Topology)	H: N-acetylmuramoyl-L-alanine amidase-like (From Topology)	T: N-acetylmuramoyl-L-alanine amidase-like	F: Amidase_2	ECOD (1.6)
B	UNK_F_TYPE	e4bxdB1	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: UNK_F_TYPE	ECOD (1.6)
B	Amidase_2	e4bxdB2	A: a+b three layers	X: N-acetylmuramoyl-L-alanine amidase-like (From Topology)	H: N-acetylmuramoyl-L-alanine amidase-like (From Topology)	T: N-acetylmuramoyl-L-alanine amidase-like	F: Amidase_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)
A	1.10.101.10	Mainly Alpha	Orthogonal Bundle	Muramoyl-pentapeptide Carboxypeptidase	domain 1	CATH (4.3.0)
B	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)
B	1.10.101.10	Mainly Alpha	Orthogonal Bundle	Muramoyl-pentapeptide Carboxypeptidase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01510	N-acetylmuramoyl-L-alanine amidase (Amidase_2)	N-acetylmuramoyl-L-alanine amidase	This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The ...	This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	AMPDH3	cation binding ion binding binding metal ion binding small molecule binding peptidoglycan muralytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity N-acetylmuramoyl-L-alanine amidase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process macromolecule metabolic process cellular component organization cell wall organization or biogenesis carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process macromolecule metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization peptidoglycan turnover	cell periphery Gram-negative-bacterium-type cell wall external encapsulating structure cell envelope cell wall cellular anatomical entity peptidoglycan-based cell wall membrane outer membrane
C, D	PEPTIDE	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036365	PGBD-like superfamily	Homologous Superfamily
A, B	IPR002502	N-acetylmuramoyl-L-alanine amidase domain	Domain
A, B	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily	Homologous Superfamily
A, B	IPR036366	PGBD superfamily	Homologous Superfamily
A, B	IPR051206	N-acetylmuramoyl-L-alanine amidase 2	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	6CL	Parent Component: LYS
C, D	DAL	RESID: AA0111 , AA0191 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862
C, D	FGA	RESID: AA0111 , AA0191

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.