1YCK

Crystal structure of human peptidoglycan recognition protein (PGRP-S)

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ycka1	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, PGRP-S	human (Homo sapiens ) [TaxId: 9606 ],	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	8021984	4001915	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8034364	3000555	SCOP2 (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	e1yckA1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	Peptidoglycan recognition protein	glycosaminoglycan binding binding carbohydrate derivative binding peptidoglycan binding protein binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity Hsp70 protein binding protein-folding chaperone binding heat shock protein binding glycosaminoglycan binding binding carbohydrate derivative binding peptidoglycan binding protein binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity Hsp70 protein binding protein-folding chaperone binding heat shock protein 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 molecular adaptor activity peptidoglycan immune receptor activity molecular transducer activity pattern recognition receptor activity signaling receptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of immune effector process multicellular organismal process regulation of leukocyte differentiation regulation of cellular process response to stimulus regulation of leukocyte activation negative regulation of biological process regulation of cell activation regulation of cell differentiation mononuclear cell differentiation natural killer cell differentiation involved in immune response lymphocyte differentiation cell activation involved in immune response regulation of cell development negative regulation of natural killer cell activation regulation of immune effector process multicellular organismal process regulation of leukocyte differentiation regulation of cellular process response to stimulus regulation of leukocyte activation negative regulation of biological process regulation of cell activation regulation of cell differentiation mononuclear cell differentiation natural killer cell differentiation involved in immune response lymphocyte differentiation cell activation involved in immune response regulation of cell development negative regulation of natural killer cell activation multicellular organism development cell differentiation anatomical structure development regulation of immune system process negative regulation of natural killer cell differentiation negative regulation of hemopoiesis regulation of natural killer cell activation natural killer cell differentiation developmental process regulation of biological process immune response negative regulation of leukocyte differentiation negative regulation of immune response negative regulation of immune effector process natural killer cell activation immune effector process regulation of response to stimulus negative regulation of lymphocyte differentiation regulation of immune response negative regulation of multicellular organismal process negative regulation of leukocyte activation leukocyte differentiation cellular developmental process regulation of developmental process cell development lymphocyte activation negative regulation of lymphocyte activation leukocyte activation regulation of natural killer cell differentiation natural killer cell activation involved in immune response leukocyte activation involved in immune response negative regulation of cellular process regulation of multicellular organismal process negative regulation of cell differentiation lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of multicellular organismal development negative regulation of response to stimulus hemopoiesis negative regulation of developmental process biological regulation cell activation negative regulation of cell activation negative regulation of cell development regulation of natural killer cell differentiation involved in immune response negative regulation of immune system process immune system process regulation of hemopoiesis cellular process negative regulation of natural killer cell differentiation involved in immune response regulation of lymphocyte activation biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response regulation of inflammatory response negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response detection of external biotic stimulus detection of biotic stimulus detection of bacterium detection of stimulus response to bacterium detection of other organism 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 humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide regulation of type II interferon production type II interferon production cellular biosynthetic process negative regulation of cellular metabolic process cytokine production regulation of cytokine production negative regulation of type II interferon production negative regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing biological process involved in interaction with host biological process involved in symbiotic interaction defense response to Gram-positive bacterium defense response to bacterium	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle phagocytic vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle phagocytic vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen endocytic vesicle lumen cytoplasm endocytic vesicle tertiary granule lumen endomembrane system tertiary granule secretory granule secretory vesicle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen specific granule lumen specific granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017331	Peptidoglycan recognition protein, PGRP-S	Family
A	IPR002502	N-acetylmuramoyl-L-alanine amidase domain	Domain
A	IPR006619	Peptidoglycan recognition protein family domain, metazoa/bacteria	Domain
A	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily	Homologous Superfamily
A	IPR015510	Peptidoglycan recognition protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O75594	Brain Injuries osteosarcoma brain injury MALT lymphoma

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.