2ZL4

Crystal structure of H.pylori ClpP S99A in complex with the peptide AAAA

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)
A	d2zl4a_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
AA [auth N]	d2zl4n_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
C [auth B]	d2zl4b_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
E [auth C]	d2zl4c_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
G [auth D]	d2zl4d_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
I [auth E]	d2zl4e_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
K [auth F]	d2zl4f_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
M [auth G]	d2zl4g_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
O [auth H]	d2zl4h_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
Q [auth I]	d2zl4i_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
S [auth J]	d2zl4j_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
U [auth K]	d2zl4k_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
W [auth L]	d2zl4l_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
Y [auth M]	d2zl4m_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	Clp protease, ClpP subunit	(Helicobacter pylori ) [TaxId: 210 ],	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	8068475	3000033	SCOP2B (2022-06-29)
AA [auth N]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
K [auth F]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
M [auth G]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
O [auth H]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
Q [auth I]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
S [auth J]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
U [auth K]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
W [auth L]	SCOP2B Superfamily	ClpP/crotonase	8068475	3000033	SCOP2B (2022-06-29)
Y [auth M]	SCOP2B Superfamily	ClpP/crotonase	8068475	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	e2zl4A1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
AA [auth N]	PF00574	e2zl4N1	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 [auth B]	PF00574	e2zl4B1	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 [auth C]	PF00574	e2zl4C1	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 [auth D]	PF00574	e2zl4D1	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 [auth E]	PF00574	e2zl4E1	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 [auth F]	PF00574	e2zl4F1	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 [auth G]	PF00574	e2zl4G1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
O [auth H]	PF00574	e2zl4H1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
Q [auth I]	PF00574	e2zl4I1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
S [auth J]	PF00574	e2zl4J1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
U [auth K]	PF00574	e2zl4K1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
W [auth L]	PF00574	e2zl4L1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
Y [auth M]	PF00574	e2zl4M1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	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 N]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
C [auth B]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
E [auth C]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
G [auth D]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
I [auth E]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
K [auth F]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
M [auth G]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
O [auth H]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
Q [auth I]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
S [auth J]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
U [auth K]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
W [auth L]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
Y [auth M]	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 N], C [auth B], E [auth C], G [auth D], A, AA [auth N], C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	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 [auth O], BA [auth 2], D [auth P], F [auth Q], H [auth R], B [auth O], BA [auth 2], D [auth P], F [auth Q], H [auth R], J [auth S], L [auth T], N [auth U], P [auth V], R [auth W], T [auth X], V [auth Y], X [auth Z], Z [auth 1]	Peptide substrate AAAA	-	-	-
A, AA [auth N], C [auth B], E [auth C], G [auth D], A, AA [auth N], C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	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	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity endopeptidase Clp complex protein-containing complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, AA [auth N], C [auth B], E [auth C], G [auth D], A, AA [auth N], C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, AA [auth N], C [auth B], E [auth C], G [auth D], A, AA [auth N], C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
A, AA [auth N], C [auth B], E [auth C], G [auth D], A, AA [auth N], C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	IPR018215	ClpP, Ser active site	Active Site
A, AA [auth N], C [auth B], E [auth C], G [auth D], A, AA [auth N], C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	IPR033135	ClpP, histidine active site	Active Site
A, AA [auth N], C [auth B], E [auth C], G [auth D], A, AA [auth N], C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	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.