Annotations: 1VH8

Crystal structure of a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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	d1vh8f1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
F	d1vh8f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
E	d1vh8e1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
E	d1vh8e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
D	d1vh8d1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
D	d1vh8d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
C	d1vh8c1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
C	d1vh8c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1vh8b1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1vh8b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1vh8a1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1vh8a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	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	8035787	3000926	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IpsF-like	8035787	3000926	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	IpsF-like	8035787	3000926	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IpsF-like	8035787	3000926	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	IpsF-like	8035787	3000926	SCOP2B (2022-06-29)
A	SCOP2 Family	IpsF-like	8023407	4003475	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IpsF-like	8035787	3000926	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)
F	Ribonuc_L-PSP	e1vh8F1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
E	Ribonuc_L-PSP	e1vh8E1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
D	Ribonuc_L-PSP	e1vh8D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
C	Ribonuc_L-PSP	e1vh8C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
B	Ribonuc_L-PSP	e1vh8B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
A	Ribonuc_L-PSP	e1vh8A1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)

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 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

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