3VM6

Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate

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	8064094	3000693	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8064094	3000693	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8064094	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	PF01008	e3vm6A3	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: PF01008	ECOD (1.6)
A	PF01008	e3vm6A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: PF01008	ECOD (1.6)
B	PF01008	e3vm6B3	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: PF01008	ECOD (1.6)
B	PF01008	e3vm6B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: PF01008	ECOD (1.6)
C	PF01008	e3vm6C3	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: PF01008	ECOD (1.6)
C	PF01008	e3vm6C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: PF01008	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	Translation initiation factor eIF-2B, delta subunit	isomerase activity S-methyl-5-thioribose-1-phosphate isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity catalytic activity ribose 1,5-bisphosphate isomerase activity	oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process cellular metabolic compound salvage methionine biosynthetic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process L-methionine salvage from methylthioadenosine proteinogenic amino acid biosynthetic process metabolic process cellular process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process monosaccharide metabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic process monosaccharide catabolic process small molecule catabolic process pentose metabolic process pentose catabolic process organic substance 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 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.