2F2L | pdb_00002f2l

Crystal structure of tracheal cytotoxin (TCT) bound to the ectodomain complex of peptidoglycan recognition proteins LCa (PGRP-LCa) and LCx (PGRP-LCx)

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2f2la2	Alpha and beta proteins (a+b)	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	automated matches	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A	d2f2la3	Artifacts	Tags	Tags	Tags	N-terminal Tags	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
B [auth X]	d2f2lx1	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-LC	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
B [auth X]	d2f2lx2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	SCOP2B Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8067273	3000555	SCOP2B (2022-06-29)
B [auth X]	SCOP2 Family	N-acetylmuramoyl-L-alanine amidase-like	8028133	4001915	SCOP2 (2022-06-29)
B [auth X]	SCOP2 Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8040512	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	e2f2lA1	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 [auth X]	Amidase_2	e2f2lX1	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 [auth X]	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
B [auth X]	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-LC isoform LCa	protein binding binding signaling receptor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway peptidoglycan recognition protein signaling pathway positive regulation of immune response response to bacterium regulation of immune system process cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway peptidoglycan recognition protein signaling pathway positive regulation of immune response response to bacterium regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process immune response response to other organism regulation of peptidoglycan recognition protein signaling pathway regulation of innate immune response response to external stimulus negative regulation of defense response to bacterium regulation of response to stimulus defense response to other organism negative regulation of response to external stimulus regulation of pattern recognition receptor signaling pathway positive regulation of defense response negative regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus signaling negative regulation of signaling positive regulation of biological process negative regulation of cell communication positive regulation of response to stimulus defense response to bacterium positive regulation of response to external stimulus negative regulation of peptidoglycan recognition protein signaling pathway immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response negative regulation of cellular process response to external biotic stimulus regulation of defense response to bacterium regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus biological regulation defense response to symbiont negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication cellular process multicellular organismal process determination of adult lifespan negative regulation of immune response humoral immune response antibacterial humoral response antimicrobial humoral response	cell periphery cellular anatomical structure plasma membrane membrane
B [auth X]	Peptidoglycan recognition protein-LC isoform LCx	glycosaminoglycan binding binding carbohydrate derivative binding peptidoglycan binding molecular transducer activity pattern recognition receptor activity signaling receptor activity lipopolysaccharide immune receptor activity peptidoglycan immune receptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding glycosaminoglycan binding binding carbohydrate derivative binding peptidoglycan binding molecular transducer activity pattern recognition receptor activity signaling receptor activity lipopolysaccharide immune receptor activity peptidoglycan immune receptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	response to stimulus immune response immune system process 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 regulation of response to external stimulus signaling positive regulation of biological process response to biotic stimulus response to stimulus immune response immune system process 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 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 response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus 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 humoral immune response antibacterial humoral response antimicrobial humoral response regulation of humoral immune response pigment metabolic process secondary metabolic process melanin metabolic process melanization defense response regulation of secondary metabolic process regulation of melanization defense response phenol-containing compound metabolic process metabolic process regulation of metabolic process antibacterial peptide production regulation of immune effector process regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria positive regulation of macromolecule biosynthetic process positive regulation of metabolic process antimicrobial humoral immune response mediated by antimicrobial peptide positive regulation of antimicrobial peptide biosynthetic process positive regulation of macromolecule metabolic process positive regulation of antibacterial peptide biosynthetic process immune effector process regulation of antimicrobial peptide biosynthetic process regulation of gene expression biosynthetic process peptide biosynthetic process antibacterial peptide biosynthetic process positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response peptide metabolic process regulation of antibacterial peptide production defense response to Gram-negative bacterium positive regulation of defense response to bacterium positive regulation of antimicrobial peptide production positive regulation of humoral immune response positive regulation of biosynthetic process antimicrobial peptide production positive regulation of immune effector process biosynthetic process of antibacterial peptides active against Gram-negative bacteria positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process regulation of defense response to bacterium regulation of antimicrobial humoral response regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of antimicrobial humoral response regulation of antimicrobial peptide production positive regulation of gene expression antimicrobial peptide biosynthetic process positive regulation of antibacterial peptide production regulation of antibacterial peptide biosynthetic process positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria regulation of synaptic plasticity trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of biological quality defense response to virus response to virus	cellular anatomical structure membrane cell periphery plasma membrane presynapse synapse cell junction apicolateral plasma membrane plasma membrane region membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle cellular anatomical structure membrane cell periphery plasma membrane presynapse synapse cell junction apicolateral plasma membrane plasma membrane region membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.