2AMT | pdb_00002amt

Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor

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)
F	d2amtf_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2amte_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2amtd_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2amtc_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2amtb_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2amta_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	IpsF-like	8039227	3000926	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IpsF-like	8039227	3000926	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	IpsF-like	8039227	3000926	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IpsF-like	8039227	3000926	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	IpsF-like	8039227	3000926	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	IpsF-like	8039227	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)
F	Hepar_II_III	e2amtF1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (develop294)
E	Hepar_II_III	e2amtE1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (develop294)
D	Hepar_II_III	e2amtD1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (develop294)
C	Hepar_II_III	e2amtC1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (develop294)
B	Hepar_II_III	e2amtB1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (develop294)
A	Hepar_II_III	e2amtA1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
E	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

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 manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding zinc ion binding phosphorus-oxygen lyase activity 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity lyase activity catalytic activity identical protein binding protein binding	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 small molecule biosynthetic process ketone metabolic process ubiquinone biosynthetic process quinone metabolic process quinone biosynthetic process small molecule metabolic process ubiquinone metabolic process ketone biosynthetic 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.