2R3Y | pdb_00002r3y

Crystal structure of the DegS protease in complex with the YWF activating peptide

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	d2r3ya1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Stress sensor protease DegS, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2r3ya2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Stress sensor protease DegS, catalytic domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2r3yc1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Stress sensor protease DegS, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2r3yc2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Stress sensor protease DegS, catalytic domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2r3yb1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Stress sensor protease DegS, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2r3yb2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Stress sensor protease DegS, catalytic domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8042458	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8042458	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8042458	3000114	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	PI3K_C2	e2r3yA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (v294.1)
C	PI3K_C2	e2r3yC1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (v294.1)
B	PI3K_C2	e2r3yB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
C	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
C	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
B	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00089	Trypsin (Trypsin)	Trypsin		Domain
A, B, C	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E, F	Synthetic peptide YWF	-	-	-
A, B, C	Protease degS	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding binding	cellular response to stimulus cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein cellular response to stress response to stimulus response to stress response to topologically incorrect protein cellular process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane extracellular region outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C	IPR001940	Peptidase S1C	Family
A, B, C	IPR036034	PDZ superfamily	Homologous Superfamily
A, B, C	IPR011783	Peptidase S1C, DegS	Family
A, B, C	IPR001478	PDZ domain	Domain
A, B, C	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown

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.