1LK5 | pdb_00001lk5

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
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)
A	SCOP2 Family	D-ribose-5-phosphate isomerase (RpiA), catalytic domain	8028955	4002307	SCOP2 (2022-06-29)
A	SCOP2 Family	D-ribose-5-phosphate isomerase (RpiA), lid domain	8028957	4002654	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	D-ribose-5-phosphate isomerase (RpiA), lid domain	8041336	3001555	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)
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)
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)
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)
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)

Domain Annotation: CATH CATH Database Homepage

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

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	monosaccharide metabolic process carbohydrate metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process pentose metabolic process D-ribose metabolic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process monosaccharide metabolic process carbohydrate metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process pentose metabolic process D-ribose metabolic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process generation of precursor metabolites and energy nucleotide metabolic process NADP+ metabolic process aldehyde metabolic process purine-containing compound metabolic process NADPH regeneration organophosphate metabolic process pentose-phosphate shunt, non-oxidative branch	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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 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.