1LK7 | pdb_00001lk7

Structure of D-Ribose-5-Phosphate Isomerase from in complex with phospho-erythronic acid

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)
D	d1lk7d1	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	d1lk7d2	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	d1lk7c1	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	d1lk7c2	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	d1lk7b1	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	d1lk7b2	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	d1lk7a1	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	d1lk7a2	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	NagB/RpiA/CoA transferase-like	8041334	3000693	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)
A	SCOP2B Superfamily	D-ribose-5-phosphate isomerase (RpiA), lid domain	8041336	3001555	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8041334	3000693	SCOP2B (2022-06-29)
A	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)
D	RNase_P_Rpp14	e1lk7D1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
D	CoA_trans	e1lk7D2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: CoA_trans	ECOD (develop294)
C	RNase_P_Rpp14	e1lk7C1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
C	CoA_trans	e1lk7C2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: CoA_trans	ECOD (develop294)
B	RNase_P_Rpp14	e1lk7B1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
B	CoA_trans	e1lk7B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: CoA_trans	ECOD (develop294)
A	RNase_P_Rpp14	e1lk7A1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
A	CoA_trans	e1lk7A2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: CoA_trans	ECOD (develop294)

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)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.