1YG8 | pdb_00001yg8

The structure of a V6A variant of ClpP.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
Z	d1yg8z_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
Y	d1yg8y_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
X	d1yg8x_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
W	d1yg8w_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
V	d1yg8v_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
U	d1yg8u_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
T	d1yg8t_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
S	d1yg8s_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
R	d1yg8r_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
Q	d1yg8q_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
P	d1yg8p_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
O	d1yg8o_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
N	d1yg8n_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
M	d1yg8m_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d1yg8l_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d1yg8k_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d1yg8j_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d1yg8i_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1yg8h_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1yg8g_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1yg8f_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1yg8e_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1yg8d_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1yg8c_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1yg8b_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1yg8a_	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)
Z	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
Y	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
X	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
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)
BA [auth b]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
AA [auth a]	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)
Z	ECH_1	e1yg8Z1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
Y	ECH_1	e1yg8Y1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
X	ECH_1	e1yg8X1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
W	ECH_1	e1yg8W1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
V	ECH_1	e1yg8V1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
U	ECH_1	e1yg8U1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
T	ECH_1	e1yg8T1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
S	ECH_1	e1yg8S1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
R	ECH_1	e1yg8R1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
Q	ECH_1	e1yg8Q1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
P	ECH_1	e1yg8P1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
O	ECH_1	e1yg8O1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
N	ECH_1	e1yg8N1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
M	ECH_1	e1yg8M1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
L	ECH_1	e1yg8L1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
K	ECH_1	e1yg8K1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
J	ECH_1	e1yg8J1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
I	ECH_1	e1yg8I1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
H	ECH_1	e1yg8H1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
G	ECH_1	e1yg8G1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
F	ECH_1	e1yg8F1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
E	ECH_1	e1yg8E1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
D	ECH_1	e1yg8D1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
C	ECH_1	e1yg8C1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
BA [auth b]	Hepar_II_III	e1yg8b1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (develop294)
B	ECH_1	e1yg8B1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)
AA [auth a]	Hepar_II_III	e1yg8a1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (develop294)
A	ECH_1	e1yg8A1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
Z	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
Y	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
X	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
W	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
V	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
U	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
T	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
S	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
R	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
Q	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
P	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
O	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
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)
BA [auth b]	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)
AA [auth a]	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	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, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR018215	ClpP, Ser active site	Active Site
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR033135	ClpP, histidine active site	Active Site