1T5O

Crystal structure of the translation initiation factor eIF-2B, subunit delta, from A. fulgidus

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)
A	d1t5oa1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative eIF-2B delta-subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
A	d1t5oa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
B	d1t5ob1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative eIF-2B delta-subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
B	d1t5ob2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
C	d1t5oc1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative eIF-2B delta-subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
C	d1t5oc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
D	d1t5od1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative eIF-2B delta-subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
D	d1t5od2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	IF2B-like	8027606	4002100	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NagB/RpiA/CoA transferase-like	8039985	3000693	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8039985	3000693	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8039985	3000693	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8039985	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	e1t5oA2	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	e1t5oA1	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	e1t5oB3	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	e1t5oB2	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	e1t5oC3	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	e1t5oC2	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)
D	IF-2B_N	e1t5oD3	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)
D	IF-2B_C	e1t5oD2	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)
D	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)
D	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, D	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, D	Translation initiation factor eIF2B, subunit delta	isomerase activity S-methyl-5-thioribose-1-phosphate isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity catalytic 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 S-adenosylmethionine metabolic process organic substance biosynthetic 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 S-adenosylmethionine metabolic process organic substance biosynthetic process sulfur compound metabolic process small molecule metabolic process L-methionine biosynthetic process cellular metabolic compound salvage S-adenosylmethionine cycle 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 L-methionine salvage from S-adenosylmethionine proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR042529	Initiation factor 2B-like, C-terminal	Homologous Superfamily
A, B, C, D	IPR037171	NagB/RpiA transferase-like	Homologous Superfamily
A, B, C, D	IPR000649	Initiation factor 2B-related	Family
A, B, C, D	IPR011559	Initiation factor 2B alpha/beta/delta	Family
A, B, C, D	IPR027363	Methylthioribose-1-phosphate isomerase, N-terminal	Homologous Superfamily
A, B, C, D	IPR005251	Methylthioribose-1-phosphate isomerase	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.