6IW7 | pdb_00006iw7

structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
N [auth G]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
L [auth N]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
K [auth M]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
B	SCOP2 Family	Clp protease, ClpP subunit	8099059	4003574	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	ClpP/crotonase	8099060	3000033	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
M [auth E]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
H [auth J]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
F [auth H]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	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)
N [auth G]	MG4	e6iw7G1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
L [auth N]	MG4	e6iw7N1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
K [auth M]	MG4	e6iw7M1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
I [auth K]	MG4	e6iw7K1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
G [auth I]	MG4	e6iw7I1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
D	MG4	e6iw7D1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
B	RhoGEF	e6iw7B1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: RhoGEF	ECOD (develop294)
M [auth E]	MG4	e6iw7E1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
J [auth L]	MG4	e6iw7L1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
H [auth J]	MG4	e6iw7J1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
F [auth H]	MG4	e6iw7H1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
E [auth F]	MG4	e6iw7F1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)
C	RhoGEF	e6iw7C1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: RhoGEF	ECOD (develop294)
A	MG4	e6iw7A1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N [auth G]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
L [auth N]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
K [auth M]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
I [auth K]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
G [auth I]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
D	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
B	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
M [auth E]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
J [auth L]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
H [auth J]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
F [auth H]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
E [auth F]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
C	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
A	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E [auth F], F [auth H], H [auth J], A, C, E [auth F], F [auth H], H [auth J], J [auth L], M [auth E]	PF00574	Clp protease (CLP_protease)	Clp protease	The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large in ...	The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, G [auth I], I [auth K], K [auth M], B, D, G [auth I], I [auth K], K [auth M], L [auth N], N [auth G]	ATP-dependent Clp protease proteolytic subunit 1	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 ATP-dependent peptidase activity ATP-dependent activity ATPase binding protein binding binding enzyme binding	catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane endopeptidase Clp complex protein-containing complex catalytic complex
A, C, E [auth F], F [auth H], H [auth J], A, C, E [auth F], F [auth H], H [auth J], J [auth L], M [auth E]	ATP-dependent Clp protease proteolytic subunit 2	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 ATP-dependent peptidase activity ATP-dependent activity ATPase binding protein binding binding enzyme binding	catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process	endopeptidase Clp complex protein-containing complex catalytic complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, G [auth I], I [auth K], K [auth M], B, D, G [auth I], I [auth K], K [auth M], L [auth N], N [auth G]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
B, D, G [auth I], I [auth K], K [auth M], B, D, G [auth I], I [auth K], K [auth M], L [auth N], N [auth G]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
B, D, G [auth I], I [auth K], K [auth M], B, D, G [auth I], I [auth K], K [auth M], L [auth N], N [auth G]	IPR033135	ClpP, histidine active site	Active Site
B, D, G [auth I], I [auth K], K [auth M], B, D, G [auth I], I [auth K], K [auth M], L [auth N], N [auth G]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
A, C, E [auth F], F [auth H], H [auth J], A, C, E [auth F], F [auth H], H [auth J], J [auth L], M [auth E]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, C, E [auth F], F [auth H], H [auth J], A, C, E [auth F], F [auth H], H [auth J], J [auth L], M [auth E]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
A, C, E [auth F], F [auth H], H [auth J], A, C, E [auth F], F [auth H], H [auth J], J [auth L], M [auth E]	IPR018215	ClpP, Ser active site	Active Site
A, C, E [auth F], F [auth H], H [auth J], A, C, E [auth F], F [auth H], H [auth J], J [auth L], M [auth E]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
A, C, E [auth F], F [auth H], H [auth J], A, C, E [auth F], F [auth H], H [auth J], J [auth L], M [auth E]	IPR033135	ClpP, histidine active site	Active Site

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.