2Z9I

Crystal structure of RV0983 from Mycobacterium tuberculosis- Proteolytically active form

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	d2z9ia1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Protease PepD	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d2z9ia2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Protease PepD	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d2z9ib1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Protease PepD	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d2z9ib2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Protease PepD	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d2z9ic1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Protease PepD	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d2z9ic2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Protease PepD	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Prokaryotic proteases	8025917	4002151	SCOP2 (2022-06-29)
A	SCOP2 Family	HtrA-like serine proteases	8025916	4002154	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Trypsin-like serine proteases	8038296	3000114	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PDZ domain-like	8038295	3000388	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8038295	3000388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8038296	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8038296	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	Trypsin_2	e2z9iA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Trypsin_2	ECOD (1.6)
A	PDZ_2	e2z9iA2	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ_2	ECOD (1.6)
B	Trypsin_2	e2z9iB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Trypsin_2	ECOD (1.6)
B	PDZ_2	e2z9iB2	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ_2	ECOD (1.6)
C	Trypsin_2	e2z9iC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Trypsin_2	ECOD (1.6)
C	PDZ_2	e2z9iC2	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ_2	ECOD (1.6)

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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF13180	PDZ domain (PDZ_2)	PDZ domain	-	Domain
A, B, C	PF13365	Trypsin-like peptidase domain (Trypsin_2)	Trypsin-like peptidase domain	This family includes trypsin-like peptidase domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	PROBABLE SERINE PROTEASE PEPD	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process cellular response to stimulus cellular response to antibiotic cellular response to chemical stimulus organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process cellular response to stimulus cellular response to antibiotic cellular response to chemical stimulus response to stimulus response to chemical cellular process response to antibiotic proteolysis	cell periphery plasma membrane membrane cellular anatomical entity extracellular region
D, E, F	SVEQV	-	-	-
G, H, I	GATV	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C	IPR001478	PDZ domain	Domain
A, B, C	IPR001940	Peptidase S1C	Family
A, B, C	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B, C	IPR036034	PDZ superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.