2YVK | pdb_00002yvk

Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis

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)
D	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8064088	3000693	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8064088	3000693	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NagB/RpiA/CoA transferase-like	8064088	3000693	SCOP2B (2022-06-29)
A	SCOP2 Family	IF2B-like	8064087	4002100	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NagB/RpiA/CoA transferase-like	8064088	3000693	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	AA_kinase	e2yvkD2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: AA_kinase	ECOD (v294.1)
C	AA_kinase	e2yvkC2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: AA_kinase	ECOD (v294.1)
B	AA_kinase	e2yvkB2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: AA_kinase	ECOD (v294.1)
A	AA_kinase	e2yvkA2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: AA_kinase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

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	Methylthioribose-1-phosphate isomerase	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 sulfur amino acid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process oxoacid metabolic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process small molecule biosynthetic 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	-

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 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.