3S04 | pdb_00003s04

Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d3s04b_	All beta proteins	LexA/Signal peptidase	LexA/Signal peptidase	Type 1 signal peptidase	Type 1 signal peptidase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3s04a_	All beta proteins	LexA/Signal peptidase	LexA/Signal peptidase	Type 1 signal peptidase	Type 1 signal peptidase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	LexA/Signal peptidase-like	8043153	3000103	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LexA/Signal peptidase-like	8043153	3000103	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)
B	Ion_trans_2	e3s04B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (develop294)
A	PI3K_C2	e3s04A2	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.10.109.10	Mainly Beta	Ribbon	Umud Fragment, subunit A	Umud Fragment, subunit A	CATH (4.3.0)
B	2.170.230.10	Mainly Beta	Beta Complex	Signal Peptidase I	Chain: A, domain 2	CATH (4.3.0)
A	2.10.109.10	Mainly Beta	Ribbon	Umud Fragment, subunit A	Umud Fragment, subunit A	CATH (4.3.0)
A	2.170.230.10	Mainly Beta	Beta Complex	Signal Peptidase I	Chain: A, domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth I], D [auth J]	Glyco-Arylomycin	-	-	-
A, B	Signal peptidase I	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity signal peptidase activity	primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019533	Peptidase S26	Domain
A, B	IPR019766	Signal peptidase I, all-beta subdomain	Homologous Superfamily
A, B	IPR019756	Peptidase S26A, signal peptidase I, serine active site	Active Site
A, B	IPR019758	Peptidase S26A, signal peptidase I, conserved site	Conserved Site
A, B	IPR019757	Peptidase S26A, signal peptidase I, lysine active site	Active Site
A, B	IPR036286	LexA/Signal peptidase-like superfamily	Homologous Superfamily
A, B	IPR000223	Peptidase S26A, signal peptidase I	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth I], D [auth J]	02V
C [auth I], D [auth J]	DAL	RESID: AA0111 , AA0191 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862
C [auth I], D [auth J]	DSE	RESID: AA0111 , AA0191

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.