6L3X

Discovery of novel peptidomimetic boronate ClpP inhibitors with noncanonical enzyme mechanism as potent virulence blockers in vitro and in vivo

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	d6l3xa_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
B	d6l3xb_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
C	d6l3xc_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
D	d6l3xd_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
E	d6l3xe_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
F	d6l3xf_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
G	d6l3xg_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
H	d6l3xh_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
I	d6l3xi_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
J	d6l3xj_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
K	d6l3xk_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
L	d6l3xl_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
M	d6l3xm_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)
N	d6l3xn_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Staphylococcus aureus RF122 ) [TaxId: 273036 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
I	SCOP2 Family	Clp protease ClpP subunit	8099313	4003574	SCOP2 (2022-06-29)
I	SCOP2 Superfamily	ClpP/crotonase	8099314	3000033	SCOP2 (2022-06-29)
J	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	ClpP/crotonase	8099314	3000033	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	ClpP/crotonase	8099314	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	PF00574	e6l3xA1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
B	PF00574	e6l3xB1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
C	PF00574	e6l3xC1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
D	PF00574	e6l3xD1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
E	PF00574	e6l3xE1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
F	PF00574	e6l3xF1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
G	PF00574	e6l3xG1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
H	PF00574	e6l3xH1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
I	PF00574	e6l3xI1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
J	PF00574	e6l3xJ1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
K	PF00574	e6l3xK1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
L	PF00574	e6l3xL1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
M	PF00574	e6l3xM1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
N	PF00574	e6l3xN1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)

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	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

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	IPR033135	ClpP, histidine 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

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 R01GM133198.