Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1VHA

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008299	biological_process	isoprenoid biosynthetic process
A	0008685	molecular_function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
A	0016114	biological_process	terpenoid biosynthetic process
A	0016829	molecular_function	lyase activity
A	0019288	biological_process	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
A	0046872	molecular_function	metal ion binding
B	0008299	biological_process	isoprenoid biosynthetic process
B	0008685	molecular_function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
B	0016114	biological_process	terpenoid biosynthetic process
B	0016829	molecular_function	lyase activity
B	0019288	biological_process	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
B	0046872	molecular_function	metal ion binding
C	0008299	biological_process	isoprenoid biosynthetic process
C	0008685	molecular_function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
C	0016114	biological_process	terpenoid biosynthetic process
C	0016829	molecular_function	lyase activity
C	0019288	biological_process	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
C	0046872	molecular_function	metal ion binding
D	0008299	biological_process	isoprenoid biosynthetic process
D	0008685	molecular_function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
D	0016114	biological_process	terpenoid biosynthetic process
D	0016829	molecular_function	lyase activity
D	0019288	biological_process	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
D	0046872	molecular_function	metal ion binding
E	0008299	biological_process	isoprenoid biosynthetic process
E	0008685	molecular_function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
E	0016114	biological_process	terpenoid biosynthetic process
E	0016829	molecular_function	lyase activity
E	0019288	biological_process	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
E	0046872	molecular_function	metal ion binding
F	0008299	biological_process	isoprenoid biosynthetic process
F	0008685	molecular_function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
F	0016114	biological_process	terpenoid biosynthetic process
F	0016829	molecular_function	lyase activity
F	0019288	biological_process	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN A 169

Chain	Residue
A	ASP9
A	HOH210
B	HOH210

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN B 169

Chain	Residue
B	ASP9
B	VAL10
C	GLU136
C	HOH216

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN C 169

Chain	Residue
C	VAL10
A	GLU136
C	ASP9

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN D 169

Chain	Residue
D	ASP9
D	VAL10
D	HOH202
E	GLU136

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN F 169

Chain	Residue
D	GLU136
F	ASP9
F	VAL10
F	HOH204

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE POP B 170

Chain	Residue
A	GLY139
A	PHE140
A	ARG143
A	ACY170
B	GLY139
B	PHE140
B	ARG143
B	ACY171
C	GLY139
C	PHE140
C	ARG143
C	ACY170

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE POP D 170

Chain	Residue
D	GLY139
D	PHE140
D	ARG143
D	ACY171
E	GLY139
E	PHE140
E	ARG143
E	ACY169
F	GLY139
F	PHE140
F	ARG143
F	ACY170

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACY A 170

Chain	Residue
A	PHE140
A	THR141
B	POP170
B	ACY171
C	ACY170

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACY B 171

Chain	Residue
A	ACY170
B	PHE140
B	THR141
B	POP170
C	ACY170

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACY C 170

Chain	Residue
A	ACY170
B	POP170
B	ACY171
C	LEU138
C	GLY139
C	PHE140
C	THR141

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACY D 171

Chain	Residue
D	PHE140
D	THR141
D	POP170
E	ACY169
F	ACY170

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACY E 169

Chain	Residue
D	POP170
D	ACY171
E	PHE140
E	THR141

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACY F 170

Chain	Residue
D	POP170
D	ACY171
F	THR135
F	LEU138
F	PHE140
F	THR141

Functional Information from PROSITE/UniProt

site_id	PS01350
Number of Residues	16
Details	ISPF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. SDGDVAlHAltDAilG

Chain	Residue	Details
A	SER36-GLY51

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	54
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00107

Chain	Residue	Details
A	ASP9
A	THR133
A	PHE140
A	ARG143
B	ASP9
B	HIS11
B	HIS35
B	HIS43
B	ASP57
B	PHE62
B	THR133
B	PHE140
B	ARG143
C	ASP9
C	HIS11
C	HIS35
C	HIS43
C	ASP57
C	PHE62
C	THR133
C	PHE140
C	ARG143
D	ASP9
D	HIS11
D	HIS35
D	HIS43
D	ASP57
D	PHE62
D	THR133
D	PHE140
D	ARG143
E	ASP9
E	HIS11
E	HIS35
E	HIS43
E	ASP57
E	PHE62
E	THR133
E	PHE140
E	ARG143
F	ASP9
F	HIS11
F	HIS35
F	HIS43
F	ASP57
F	PHE62
F	THR133
F	PHE140
F	ARG143
A	HIS11
A	HIS35
A	HIS43
A	ASP57
A	PHE62

site_id	SWS_FT_FI2
Number of Residues	12
Details	SITE: Transition state stabilizer => ECO:0000255\|HAMAP-Rule:MF_00107

Chain	Residue	Details
D	HIS35
D	THR134
E	HIS35
E	THR134
F	HIS35
F	THR134
A	HIS35
A	THR134
B	HIS35
B	THR134
C	HIS35
C	THR134

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)