1LK5

Structure of the D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1lk5a1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d1lk5a2	Alpha and beta proteins (a+b)	Ferredoxin-like	D-ribose-5-phosphate isomerase (RpiA), lid domain	D-ribose-5-phosphate isomerase (RpiA), lid domain	D-ribose-5-phosphate isomerase (RpiA), lid domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1lk5b1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1lk5b2	Alpha and beta proteins (a+b)	Ferredoxin-like	D-ribose-5-phosphate isomerase (RpiA), lid domain	D-ribose-5-phosphate isomerase (RpiA), lid domain	D-ribose-5-phosphate isomerase (RpiA), lid domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
C	d1lk5c1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
C	d1lk5c2	Alpha and beta proteins (a+b)	Ferredoxin-like	D-ribose-5-phosphate isomerase (RpiA), lid domain	D-ribose-5-phosphate isomerase (RpiA), lid domain	D-ribose-5-phosphate isomerase (RpiA), lid domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
D	d1lk5d1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
D	d1lk5d2	Alpha and beta proteins (a+b)	Ferredoxin-like	D-ribose-5-phosphate isomerase (RpiA), lid domain	D-ribose-5-phosphate isomerase (RpiA), lid domain	D-ribose-5-phosphate isomerase (RpiA), lid domain	(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)
A	SCOP2 Family	D-ribose-5-phosphate isomerase (RpiA) lid domain	8028957	4002654	SCOP2 (2022-06-29)
A	SCOP2 Family	D-ribose-5-phosphate isomerase (RpiA) catalytic domain	8028955	4002307	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	D-ribose-5-phosphate isomerase (RpiA) lid domain	8041336	3001555	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	D-ribose-5-phosphate isomerase (RpiA) lid domain	8041336	3001555	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-ribose-5-phosphate isomerase (RpiA) lid domain	8041336	3001555	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	D-ribose-5-phosphate isomerase (RpiA) lid domain	8041336	3001555	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	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	Rib_5-P_isom_A_C	e1lk5A1	A: a+b two layers	X: Alpha-beta plaits	H: D-ribose-5-phosphate isomerase (RpiA), lid domain (From Topology)	T: D-ribose-5-phosphate isomerase (RpiA), lid domain	F: Rib_5-P_isom_A_C	ECOD (1.6)
A	Rib_5-P_isom_A_N	e1lk5A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: Rib_5-P_isom_A_N	ECOD (1.6)
B	Rib_5-P_isom_A_C	e1lk5B1	A: a+b two layers	X: Alpha-beta plaits	H: D-ribose-5-phosphate isomerase (RpiA), lid domain (From Topology)	T: D-ribose-5-phosphate isomerase (RpiA), lid domain	F: Rib_5-P_isom_A_C	ECOD (1.6)
B	Rib_5-P_isom_A_N	e1lk5B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: Rib_5-P_isom_A_N	ECOD (1.6)
C	Rib_5-P_isom_A_C	e1lk5C1	A: a+b two layers	X: Alpha-beta plaits	H: D-ribose-5-phosphate isomerase (RpiA), lid domain (From Topology)	T: D-ribose-5-phosphate isomerase (RpiA), lid domain	F: Rib_5-P_isom_A_C	ECOD (1.6)
C	Rib_5-P_isom_A_N	e1lk5C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: Rib_5-P_isom_A_N	ECOD (1.6)
D	Rib_5-P_isom_A_C	e1lk5D1	A: a+b two layers	X: Alpha-beta plaits	H: D-ribose-5-phosphate isomerase (RpiA), lid domain (From Topology)	T: D-ribose-5-phosphate isomerase (RpiA), lid domain	F: Rib_5-P_isom_A_C	ECOD (1.6)
D	Rib_5-P_isom_A_N	e1lk5D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: Rib_5-P_isom_A_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)
B	3.40.50.1360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)
C	3.40.50.1360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)
D	3.40.50.1360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF06026	Ribose 5-phosphate isomerase A (phosphoriboisomerase A) (Rib_5-P_isom_A)	Ribose 5-phosphate isomerase A (phosphoriboisomerase A)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	D-Ribose-5-Phosphate Isomerase	isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity ribose-5-phosphate isomerase activity catalytic activity	ribose phosphate metabolic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process organic substance metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process cellular aldehyde metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate metabolic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process organic substance metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process cellular aldehyde metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process generation of precursor metabolites and energy nucleotide metabolic process purine-containing compound metabolic process NADP metabolic process organic cyclic compound metabolic process NADPH regeneration organophosphate metabolic process metabolic process cellular process pentose-phosphate shunt, non-oxidative branch	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR037171	NagB/RpiA transferase-like	Homologous Superfamily
A, B, C, D	IPR020672	Ribose-5-phosphate isomerase, type A, subgroup	Family
A, B, C, D	IPR004788	Ribose 5-phosphate isomerase, type A	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.