1OBA | pdb_00001oba

Multimodular Pneumococcal Cell Wall Endolysin from phage Cp-1 complexed with choline

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1obaa1	All beta proteins	beta-hairpin stack	Cell wall binding repeat	Cell wall binding repeat	C-terminal domain of endolysin	(Streptococcus phage Cp1 ) [TaxId: 10747 ],	SCOPe (2.08)
A	d1obaa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	1,4-beta-N-acetylmuraminidase	N-terminal domain of endolysin	(Streptococcus phage Cp1 ) [TaxId: 10747 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	(Trans)glycosidases	8034639	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cell wall binding repeat	8034638	3000365	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	Cloacin	e1obaA1	A: a/b three-layered sandwiches	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Cloacin translocation domain	F: Cloacin	ECOD (v294.1)
A	DUF711	e1obaA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.10.270.10	Mainly Beta	Ribbon	left handed beta-beta-3-solenoid	Cholin Binding	CATH (4.3.0)
A	2.20.120.10	Mainly Beta	Single Sheet	Multimodular pneumococcal cell wall endolysin, domain 3	Multimodular pneumococcal cell wall endolysin, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01183	Glycosyl hydrolases family 25 (Glyco_hydro_25)	Glycosyl hydrolases family 25		Domain
A	PF01473	Putative cell wall binding repeat (Choline_bind_1)	Putative cell wall binding repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	LYSOZYME	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus 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 cellular process macromolecule metabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis exit from host cell viral process cytolysis in another organism viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018077	Glycoside hydrolase, family 25 subgroup	Family
A	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A	IPR002053	Glycoside hydrolase, family 25	Family
A	IPR008270	Glycosyl hydrolases family 25, active site	Active Site
A	IPR018337	Cell wall/choline-binding repeat	Repeat

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	lysozyme (glycosyl hydrolase 25 family) M-CSA #774	Cpl-1 lysin from Bacteriophage cp-1 catalyses the hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of prokaryote cell walls. On binding to choline, the enzymes geometry changes, its specificity increases, and catalytic activity is increased. Cpl-1 is used against bacteria such as Streptococcus pneumoniae (which causes pneumonia), as it kills the bacteria by breaking down its cell wall.	Defined by 4 residues: ASP:A-10ASP:A-92GLU:A-94ASP:A-182 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.2.1.17 (PDB Primary Data) Search M-CSA Motif + EC 3.2.1.17

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.

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