5HNM | pdb_00005hnm

Crystal structure of vancomycin resistance D,D-pentapeptidase VanY E175A mutant from VanB-type resistance cassette in complex with Zn(II)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Ribosomal_S2	e5hnmF1	A: alpha arrays	X: TIM beta/alpha-barrel	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_S2	ECOD (v295.2)
E	Ribosomal_S2	e5hnmE1	A: alpha arrays	X: TIM beta/alpha-barrel	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_S2	ECOD (v295.2)
D	Ribosomal_S2	e5hnmD1	A: alpha arrays	X: TIM beta/alpha-barrel	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_S2	ECOD (v295.2)
C	Ribosomal_S2	e5hnmC1	A: alpha arrays	X: TIM beta/alpha-barrel	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_S2	ECOD (v295.2)
B	Ribosomal_S2	e5hnmB1	A: alpha arrays	X: TIM beta/alpha-barrel	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_S2	ECOD (v295.2)
A	Ribosomal_S2	e5hnmA1	A: alpha arrays	X: TIM beta/alpha-barrel	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_S2	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

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

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B, C, D, E A, B, C, D, E, F	ARO:3002956	vanY gene in vanB cluster	Also known as vanYB, is a vanY variant found in the vanB gene cluster.	CARD (4.0.2)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A, B, C, D, E A, B, C, D, E, F	ARO:3000234	glycopeptide resistance gene cluster	peptide antibiotic, glycopeptide antibiotic, nonribosomal peptide antibiotics	antibiotic target alteration	CARD (4.0.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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 A, B, C, D, E, F	D-alanyl-D-alanine carboxypeptidase	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR052179	D-alanyl-D-alanine carboxypeptidase-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR009045	Peptidase M74/Hedgehog-like, zinc-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR058193	D-alanyl-D-alanine carboxypeptidase/YodJ, core domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003709	D-alanyl-D-alanine carboxypeptidase-like, core domain	Domain