4UZ2 | pdb_00004uz2

Crystal structure of the N-terminal LysM domains from the putative NlpC/P60 D,L endopeptidase from T. thermophilus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	d4uz2d1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d4uz2c1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d4uz2b1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d4uz2a1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	LysM domain-like	8076155	3001938	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LysM domain-like	8076155	3001938	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LysM domain-like	8076155	3001938	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LysM domain-like	8076155	3001938	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)
D	tRNA-synt_1_2	e4uz2D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)
C	tRNA-synt_1_2	e4uz2C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)
B	tRNA-synt_1_2	e4uz2B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)
A	Vinculin	e4uz2A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Osmotin-like	T: Osmotin-like	F: Vinculin	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01476	LysM domain (LysM)	LysM domain	The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation [1]. This domain may have a general peptidoglycan binding function. The structure of this domain is known [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN	cysteine-type peptidase activity 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR052062	Murein DD-endopeptidase/LD-carboxypeptidase	Family
A, B, C, D	IPR000064	Endopeptidase, NLPC/P60 domain	Domain
A, B, C, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D	IPR036779	LysM domain superfamily	Homologous Superfamily
A, B, C, D	IPR018392	LysM domain	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.