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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Peptidase_M42	e1yloA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Peptidase_M42	ECOD (1.6)
A	Peptidase_M20_1st	e1yloA2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: Peptidase_M20_1st	ECOD (1.6)
B	Peptidase_M42	e1yloB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Peptidase_M42	ECOD (1.6)
B	Peptidase_M20_1st	e1yloB2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: Peptidase_M20_1st	ECOD (1.6)
C	Peptidase_M42	e1yloC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Peptidase_M42	ECOD (1.6)
C	Peptidase_M20_1st	e1yloC2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: Peptidase_M20_1st	ECOD (1.6)
D	Peptidase_M42	e1yloD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Peptidase_M42	ECOD (1.6)
D	Peptidase_M20_1st	e1yloD2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: Peptidase_M20_1st	ECOD (1.6)
F	Peptidase_M42	e1yloF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Peptidase_M42	ECOD (1.6)
F	Peptidase_M20_1st	e1yloF2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: Peptidase_M20_1st	ECOD (1.6)
E	Peptidase_M42	e1yloE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Peptidase_M42	ECOD (1.6)
E	Peptidase_M20_1st	e1yloE2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: Peptidase_M20_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
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)

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.