2FZS | pdb_00002fzs

Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site

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)
N	d2fzsn_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
M	d2fzsm_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d2fzsl_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d2fzsk_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d2fzsj_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d2fzsi_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d2fzsh_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2fzsg_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2fzsf_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2fzse_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2fzsd_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2fzsc_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2fzsb_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2fzsa_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(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)
N	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ClpP/crotonase	8034397	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		e2fzsN1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
M		e2fzsM1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
L		e2fzsL1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
K		e2fzsK1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
J		e2fzsJ1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
I		e2fzsI1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
H		e2fzsH1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
G		e2fzsG1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
F		e2fzsF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
E		e2fzsE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
D		e2fzsD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
C		e2fzsC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
B		e2fzsB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)
A		e2fzsA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: ECH_1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
M	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
L	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
K	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
J	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
I	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
H	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
G	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
F	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
E	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
D	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
C	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
B	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
A	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	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
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	ATP-dependent Clp protease proteolytic subunit	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 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 identical protein binding	regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process cellular process regulation of programmed cell death cell death programmed cell death positive regulation of cellular process catabolic process proteasomal protein catabolic process metabolic process primary metabolic process regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process cellular process regulation of programmed cell death cell death programmed cell death positive regulation of cellular process catabolic process proteasomal protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process response to stimulus response to radiation response to abiotic stimulus response to stress response to heat response to temperature stimulus protein quality control for misfolded or incompletely synthesized proteins	cellular anatomical structure membrane protein-containing complex intracellular anatomical structure catalytic complex peptidase complex cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex cytoplasm cytosol intracellular protein-containing complex endopeptidase Clp complex

InterPro: Protein Family Classification InterPro Database Homepage

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