1Y8T | pdb_00001y8t

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)
C	d1y8tc1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Protease PepD	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
C	d1y8tc2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Protease PepD	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d1y8tb1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Protease PepD	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d1y8tb2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Protease PepD	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d1y8ta1	All beta proteins	PDZ domain-like	PDZ domain-like	HtrA-like serine proteases	Protease PepD	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d1y8ta2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Prokaryotic proteases	Protease PepD	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8038296	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8038296	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8038295	3000388	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8038296	3000114	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PDZ domain-like	8038295	3000388	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)
C	tRNA-synt_1b	e1y8tC1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: tRNA-synt_1b	ECOD (develop294)
B	tRNA-synt_1b	e1y8tB1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: tRNA-synt_1b	ECOD (develop294)
A	Trypsin	e1y8tA1	A: alpha bundles	X: Cloacin translocation domain	H: LigT-related	T: LigT-related	F: Trypsin	ECOD (develop294)
A	PDZ_2	e1y8tA2	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: PDZ_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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	hypothetical protein Rv0983	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	cellular response to stimulus cellular response to antibiotic cellular response to chemical stimulus response to stimulus response to chemical cellular process response to antibiotic catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule 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 catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process proteolysis	cellular anatomical structure extracellular region cell periphery plasma membrane membrane

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	IPR051201	Chloroplastic and Bacterial Serine Proteases	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.