5DKP | pdb_00005dkp

Crystal Structure of N. meningitidis ClpP in complex with agonist ADEP A54556.

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
AA [auth m]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
BA [auth n]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
K	SCOP2 Family	Clp protease, ClpP subunit	8068486	4003574	SCOP2 (2022-06-29)
K	SCOP2 Superfamily	ClpP/crotonase	8068487	3000033	SCOP2 (2022-06-29)
L	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
O [auth a]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
P [auth b]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
Q [auth c]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
R [auth d]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
S [auth e]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
T [auth f]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
U [auth g]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
V [auth h]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
W [auth i]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
X [auth j]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
Y [auth k]	SCOP2B Superfamily	ClpP/crotonase	8068487	3000033	SCOP2B (2022-06-29)
Z [auth l]	SCOP2B Superfamily	ClpP/crotonase	8068487	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)
A	CLP_protease	e5dkpA1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
AA [auth m]	CLP_protease	e5dkpm1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
B	CLP_protease	e5dkpB1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
BA [auth n]	CLP_protease	e5dkpn1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
C	CLP_protease	e5dkpC1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
D	CLP_protease	e5dkpD1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
E	CLP_protease	e5dkpE1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
F	CLP_protease	e5dkpF1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
G	CLP_protease	e5dkpG1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
H	CLP_protease	e5dkpH1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
I	CLP_protease	e5dkpI1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
J	CLP_protease	e5dkpJ1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
K	CLP_protease	e5dkpK1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
L	CLP_protease	e5dkpL1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
M	CLP_protease	e5dkpM1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
N	CLP_protease	e5dkpN1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
O [auth a]	CLP_protease	e5dkpa1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
P [auth b]	CLP_protease	e5dkpb1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
Q [auth c]	CLP_protease	e5dkpc1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
R [auth d]	CLP_protease	e5dkpd1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
S [auth e]	CLP_protease	e5dkpe1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
T [auth f]	CLP_protease	e5dkpf1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
U [auth g]	CLP_protease	e5dkpg1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
V [auth h]	CLP_protease	e5dkph1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
W [auth i]	CLP_protease	e5dkpi1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
X [auth j]	CLP_protease	e5dkpj1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
Y [auth k]	CLP_protease	e5dkpk1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)
Z [auth l]	CLP_protease	e5dkpl1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: CLP_protease	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
AA [auth m]	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)
BA [auth n]	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)
D	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)
F	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)
H	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)
J	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)
L	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)
N	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
O [auth a]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
P [auth b]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
Q [auth c]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
R [auth d]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
S [auth e]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
T [auth f]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
U [auth g]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
V [auth h]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
W [auth i]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
X [auth j]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
Y [auth k]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
Z [auth l]	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, AA [auth m], B, BA [auth n], C, A, AA [auth m], B, BA [auth n], C, D, E, F, G, H, I, J, K, L, M, N, O [auth a], P [auth b], Q [auth c], R [auth d], S [auth e], T [auth f], U [auth g], V [auth h], W [auth i], X [auth j], Y [auth k], Z [auth l]	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, AA [auth m], B, BA [auth n], C, A, AA [auth m], B, BA [auth n], C, D, E, F, G, H, I, J, K, L, M, N, O [auth a], P [auth b], Q [auth c], R [auth d], S [auth e], T [auth f], U [auth g], V [auth h], W [auth i], X [auth j], Y [auth k], Z [auth l]	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	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins	cellular anatomical structure intracellular anatomical structure cytoplasm endopeptidase Clp complex protein-containing complex catalytic complex
AB [auth 0], BB [auth 1], CA [auth O], CB [auth 2], DA [auth P], AB [auth 0], BB [auth 1], CA [auth O], CB [auth 2], DA [auth P], DB [auth 3], EA [auth Q], FA [auth R], GA [auth S], HA [auth T], IA [auth U], JA [auth V], KA [auth W], LA [auth X], MA [auth Y], NA [auth Z], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]	agonist ADEP A54556	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, AA [auth m], B, BA [auth n], C, A, AA [auth m], B, BA [auth n], C, D, E, F, G, H, I, J, K, L, M, N, O [auth a], P [auth b], Q [auth c], R [auth d], S [auth e], T [auth f], U [auth g], V [auth h], W [auth i], X [auth j], Y [auth k], Z [auth l]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, AA [auth m], B, BA [auth n], C, A, AA [auth m], B, BA [auth n], C, D, E, F, G, H, I, J, K, L, M, N, O [auth a], P [auth b], Q [auth c], R [auth d], S [auth e], T [auth f], U [auth g], V [auth h], W [auth i], X [auth j], Y [auth k], Z [auth l]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
A, AA [auth m], B, BA [auth n], C, A, AA [auth m], B, BA [auth n], C, D, E, F, G, H, I, J, K, L, M, N, O [auth a], P [auth b], Q [auth c], R [auth d], S [auth e], T [auth f], U [auth g], V [auth h], W [auth i], X [auth j], Y [auth k], Z [auth l]	IPR018215	ClpP, Ser active site	Active Site
A, AA [auth m], B, BA [auth n], C, A, AA [auth m], B, BA [auth n], C, D, E, F, G, H, I, J, K, L, M, N, O [auth a], P [auth b], Q [auth c], R [auth d], S [auth e], T [auth f], U [auth g], V [auth h], W [auth i], X [auth j], Y [auth k], Z [auth l]	IPR033135	ClpP, histidine active site	Active Site
A, AA [auth m], B, BA [auth n], C, A, AA [auth m], B, BA [auth n], C, D, E, F, G, H, I, J, K, L, M, N, O [auth a], P [auth b], Q [auth c], R [auth d], S [auth e], T [auth f], U [auth g], V [auth h], W [auth i], X [auth j], Y [auth k], Z [auth l]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
AB [auth 0], BB [auth 1], CA [auth O], CB [auth 2], DA [auth P], AB [auth 0], BB [auth 1], CA [auth O], CB [auth 2], DA [auth P], DB [auth 3], EA [auth Q], FA [auth R], GA [auth S], HA [auth T], IA [auth U], JA [auth V], KA [auth W], LA [auth X], MA [auth Y], NA [auth Z], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]	MAA	Parent Component: ALA RESID: AA0061 PSI-MOD : N-methyl-L-alanine MOD:00070
AB [auth 0], BB [auth 1], CA [auth O], CB [auth 2], DA [auth P], AB [auth 0], BB [auth 1], CA [auth O], CB [auth 2], DA [auth P], DB [auth 3], EA [auth Q], FA [auth R], GA [auth S], HA [auth T], IA [auth U], JA [auth V], KA [auth W], LA [auth X], MA [auth Y], NA [auth Z], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]	MP8	Parent Component: PRO RESID: AA0061
AB [auth 0], BB [auth 1], CA [auth O], CB [auth 2], DA [auth P], AB [auth 0], BB [auth 1], CA [auth O], CB [auth 2], DA [auth P], DB [auth 3], EA [auth Q], FA [auth R], GA [auth S], HA [auth T], IA [auth U], JA [auth V], KA [auth W], LA [auth X], MA [auth Y], NA [auth Z], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]	OTT	RESID: AA0061