2DYY | pdb_00002dyy

Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
L	d2dyyl_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
K	d2dyyk_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
J	d2dyyj_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
I	d2dyyi_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
H	d2dyyh_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
G	d2dyyg_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
F	d2dyyf_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
E	d2dyye_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
D	d2dyyd_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
C	d2dyyc_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d2dyyb_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d2dyya_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
E	SCOP2 Family	YjgF/L-PSP	8059818	4001510	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	YjgF-like	8059819	3001733	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YjgF-like	8059819	3001733	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YjgF-like	8059819	3001733	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)
L	Ribonuc_L-PSP	e2dyyL1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
K	Ribonuc_L-PSP	e2dyyK1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
J	Ribonuc_L-PSP	e2dyyJ1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
I	Ribonuc_L-PSP	e2dyyI1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
H	Ribonuc_L-PSP	e2dyyH1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
G	Ribonuc_L-PSP	e2dyyG1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
F	Ribonuc_L-PSP	e2dyyF1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
E	Ribonuc_L-PSP	e2dyyE1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
D	Ribonuc_L-PSP	e2dyyD1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
C	Ribonuc_L-PSP	e2dyyC1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
B	Ribonuc_L-PSP	e2dyyB1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
A	Ribonuc_L-PSP	e2dyyA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
K	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
J	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
I	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
H	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
G	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
F	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
E	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
D	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
C	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
B	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
A	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)

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	UPF0076 protein PH0854	hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	IPR019897	RidA, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006056	RidA family	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR035959	RutC-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006175	YjgF/YER057c/UK114 family	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.