2CB3

Crystal structure of peptidoglycan recognition protein-LE in complex with tracheal cytotoxin (monomeric diaminopimelic acid-type peptidoglycan)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2cb3a1	Alpha and beta proteins (a+b)	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	Peptidoglycan-recognition protein-LE	FRUIT FLY (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
B	d2cb3b_	Alpha and beta proteins (a+b)	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	automated matches	FRUIT FLY (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
C	d2cb3c_	Alpha and beta proteins (a+b)	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	automated matches	FRUIT FLY (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
D	d2cb3d_	Alpha and beta proteins (a+b)	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	automated matches	FRUIT FLY (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	N-acetylmuramoyl-L-alanine amidase-like	8026240	4001915	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8038619	3000555	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8038619	3000555	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8038619	3000555	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8038619	3000555	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	Amidase_2	e2cb3A1	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	Amidase_2	e2cb3B1	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)
C	Amidase_2	e2cb3C1	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)
D	Amidase_2	e2cb3D1	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)
B	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)
C	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)
D	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, C, D	PEPTIDOGLYCAN-RECOGNITION PROTEIN-LE	glycosaminoglycan binding binding carbohydrate derivative binding peptidoglycan binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	multicellular organismal process determination of adult lifespan cellular response to stimulus regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus signaling positive regulation of biological process response to biotic stimulus multicellular organismal process determination of adult lifespan cellular response to stimulus regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus signaling positive regulation of biological process response to biotic stimulus cell communication positive regulation of response to stimulus defense response to bacterium immune response-activating signaling pathway peptidoglycan recognition protein signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress response to bacterium innate immune response regulation of immune system process response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response cellular process activation of immune response defense response to Gram-negative bacterium regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis defense response to virus response to virus defense response to Gram-positive bacterium	extracellular region cellular anatomical entity intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002502	N-acetylmuramoyl-L-alanine amidase domain	Domain
A, B, C, D	IPR006619	Peptidoglycan recognition protein family domain, metazoa/bacteria	Domain
A, B, C, D	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily	Homologous Superfamily
A, B, C, D	IPR015510	Peptidoglycan recognition protein	Family

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.