5IWY | pdb_00005iwy

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d5iwya_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
C	d5iwyc_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
F	d5iwyf_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
E	d5iwye_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
D	d5iwyd_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d5iwyb_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	IpsF-like	8081210	3000926	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	Sigma70_r4_2	e5iwyA1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)
C	Sigma70_r4_2	e5iwyC1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)
F	Sigma70_r4_2	e5iwyF1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)
E	Sigma70_r4_2	e5iwyE1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)
D	Sigma70_r4_2	e5iwyD1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)
B	Sigma70_r4_2	e5iwyB1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02542	YgbB family (YgbB)	YgbB family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	cation binding ion binding binding metal ion binding small molecule binding phosphorus-oxygen lyase activity 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity lyase activity catalytic activity	isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process terpenoid biosynthetic process terpenoid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036571	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003526	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020555	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site	Conserved Site

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.