1YLO | pdb_00001ylo

Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 from Shigella flexneri 2a str. 2457T

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)
F	d1ylof1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Aminopeptidase/glucanase lid domain	Aminopeptidase/glucanase lid domain	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
F	d1ylof2	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
F	d1ylof3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
E	d1yloe1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Aminopeptidase/glucanase lid domain	Aminopeptidase/glucanase lid domain	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
E	d1yloe2	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
E	d1yloe3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
D	d1ylod1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Aminopeptidase/glucanase lid domain	Aminopeptidase/glucanase lid domain	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
D	d1ylod2	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
D	d1ylod3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
C	d1yloc1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Aminopeptidase/glucanase lid domain	Aminopeptidase/glucanase lid domain	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
C	d1yloc2	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
C	d1yloc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
B	d1ylob1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Aminopeptidase/glucanase lid domain	Aminopeptidase/glucanase lid domain	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
B	d1ylob2	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
B	d1ylob3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
A	d1yloa1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Aminopeptidase/glucanase lid domain	Aminopeptidase/glucanase lid domain	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
A	d1yloa2	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Aminopeptidase YpdE	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)
A	d1yloa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shigella flexneri 2a str. 2457T ) [TaxId: 198215 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Aminopeptidase/glucanase lid domain	8034729	3001917	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Aminopeptidase/glucanase lid domain	8034729	3001917	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Aminopeptidase/glucanase lid domain	8034729	3001917	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aminopeptidase/glucanase lid domain	8034729	3001917	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aminopeptidase/glucanase lid domain	8034729	3001917	SCOP2B (2022-06-29)
A	SCOP2 Family	Aminopeptidase/glucanase lid domain	8022349	4000893	SCOP2 (2022-06-29)
A	SCOP2 Family	Bacterial dinuclear zinc exopeptidases	8022350	4000587	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aminopeptidase/glucanase lid domain	8034729	3001917	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Zn-dependent exopeptidases	8034730	3000662	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Peptidase_S46, Trypsin_2	e1yloF1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (v294.1)
F	NAD_binding_1	e1yloF2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (v294.1)
E	Peptidase_S46, Trypsin_2	e1yloE1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (v294.1)
E	NAD_binding_1	e1yloE2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (v294.1)
D	Peptidase_S46, Trypsin_2	e1yloD1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (v294.1)
D	NAD_binding_1	e1yloD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (v294.1)
C	Peptidase_S46, Trypsin_2	e1yloC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (v294.1)
C	NAD_binding_1	e1yloC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (v294.1)
B	Peptidase_S46, Trypsin_2	e1yloB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (v294.1)
B	NAD_binding_1	e1yloB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (v294.1)
A	Peptidase_M42	e1yloA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Peptidase_M42	ECOD (v294.1)
A	Peptidase_M28	e1yloA2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Peptidase_M28	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
F	2.40.30.40	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
E	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
E	2.40.30.40	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
D	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
D	2.40.30.40	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
C	2.40.30.40	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
B	2.40.30.40	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
A	2.40.30.40	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	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	PF05343	M42 glutamyl aminopeptidase (Peptidase_M42)	M42 glutamyl aminopeptidase	-	Family

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	hypothetical protein SF2450	cation binding ion binding binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein aminopeptidase activity hydrolase activity exopeptidase activity catalytic activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR023367	Peptidase M42, domain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR051464	Peptidase M42 aminopeptidase	Family
A, B, C, D, E A, B, C, D, E, F	IPR008007	Peptidase M42	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.