4ZYB

High resolution structure of M23 peptidase LytM with substrate analogue

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Duplicated hybrid motif	8040056	3001927	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Duplicated hybrid motif	8040056	3001927	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Duplicated hybrid motif	8040056	3001927	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Duplicated hybrid motif	8040056	3001927	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	PF01551	e4zybA1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Duplicated hybrid motif	F: PF01551	ECOD (1.6)
B	PF01551	e4zybB1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Duplicated hybrid motif	F: PF01551	ECOD (1.6)
C	PF01551	e4zybC1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Duplicated hybrid motif	F: PF01551	ECOD (1.6)
D	PF01551	e4zybD1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Duplicated hybrid motif	F: PF01551	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.70.10	Mainly Beta	Distorted Sandwich	Glucose Permease (Domain IIA)	Glucose Permease (Domain IIA)	CATH (4.3.0)
B	2.70.70.10	Mainly Beta	Distorted Sandwich	Glucose Permease (Domain IIA)	Glucose Permease (Domain IIA)	CATH (4.3.0)
C	2.70.70.10	Mainly Beta	Distorted Sandwich	Glucose Permease (Domain IIA)	Glucose Permease (Domain IIA)	CATH (4.3.0)
D	2.70.70.10	Mainly Beta	Distorted Sandwich	Glucose Permease (Domain IIA)	Glucose Permease (Domain IIA)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01551	Peptidase family M23 (Peptidase_M23)	Peptidase family M23	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glycyl-glycine endopeptidase LytM	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding manganese ion binding nickel cation binding zinc ion binding peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding manganese ion binding nickel cation binding zinc ion binding peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity	cellular catabolic process organic substance metabolic process catabolic process cellular metabolic process metabolic process cellular process organic substance catabolic process peptide metabolic process peptide catabolic process organonitrogen compound metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process cellular catabolic process organic substance metabolic process catabolic process cellular metabolic process metabolic process cellular process organic substance catabolic process peptide metabolic process peptide catabolic process organonitrogen compound metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR016047	Peptidase M23	Domain
A, B, C, D	IPR011055	Duplicated hybrid motif	Homologous Superfamily

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.