5YGA

Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate, AMP and GMP

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8064096	3000693	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8064096	3000693	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8064096	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	IF-2B_N	e5ygaA1	A: alpha bundles	X: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	H: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	T: Translation initiation factor eIF-2B delta subunit N-terminal helical domain	F: IF-2B_N	ECOD (1.6)
A	IF-2B_C	e5ygaA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: IF-2B_C	ECOD (1.6)
B	IF-2B_N	e5ygaB1	A: alpha bundles	X: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	H: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	T: Translation initiation factor eIF-2B delta subunit N-terminal helical domain	F: IF-2B_N	ECOD (1.6)
B	IF-2B_C	e5ygaB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: IF-2B_C	ECOD (1.6)
C	IF-2B_N	e5ygaC1	A: alpha bundles	X: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	H: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	T: Translation initiation factor eIF-2B delta subunit N-terminal helical domain	F: IF-2B_N	ECOD (1.6)
C	IF-2B_C	e5ygaC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: IF-2B_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.420	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	translation initiation factor eif-2b, domain 1	CATH (4.3.0)
A	3.40.50.10470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor eif-2b	CATH (4.3.0)
B	1.20.120.420	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	translation initiation factor eif-2b, domain 1	CATH (4.3.0)
B	3.40.50.10470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor eif-2b	CATH (4.3.0)
C	1.20.120.420	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	translation initiation factor eif-2b, domain 1	CATH (4.3.0)
C	3.40.50.10470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor eif-2b	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01008	Initiation factor 2 subunit family (IF-2B)	Initiation factor 2 subunit family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Ribose 1,5-bisphosphate isomerase	ribose 1,5-bisphosphate isomerase activity isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity catalytic activity	monosaccharide metabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic process primary metabolic process small molecule metabolic process metabolic process monosaccharide catabolic process small molecule catabolic process pentose metabolic process pentose catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR005250	Ribose-1,5-bisphosphate isomerase	Family
A, B, C	IPR042529	Initiation factor 2B-like, C-terminal	Homologous Superfamily
A, B, C	IPR037171	NagB/RpiA transferase-like	Homologous Superfamily
A, B, C	IPR000649	Initiation factor 2B-related	Family
A, B, C	IPR011559	Initiation factor 2B alpha/beta/delta	Family
A, B, C	IPR027363	Methylthioribose-1-phosphate isomerase, N-terminal	Homologous Superfamily

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.