Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1GX1

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0006744	biological_process	ubiquinone biosynthetic process
A	0008270	molecular_function	zinc ion binding
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	0030145	molecular_function	manganese ion binding
A	0042802	molecular_function	identical protein binding
A	0046872	molecular_function	metal ion binding
B	0005515	molecular_function	protein binding
B	0006744	biological_process	ubiquinone biosynthetic process
B	0008270	molecular_function	zinc 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	0030145	molecular_function	manganese ion binding
B	0042802	molecular_function	identical protein binding
B	0046872	molecular_function	metal ion binding
C	0005515	molecular_function	protein binding
C	0006744	biological_process	ubiquinone biosynthetic process
C	0008270	molecular_function	zinc 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	0030145	molecular_function	manganese ion binding
C	0042802	molecular_function	identical protein binding
C	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A1157

Chain	Residue
A	ASP8
A	HIS10
A	HIS42
B	CDP1157

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN A1159

Chain	Residue
A	GLU135
A	CDP1158
A	HOH2090
A	HOH2091
A	HOH2092

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN B1158

Chain	Residue
B	GLU135
B	CDP1157
B	HOH2100
B	HOH2101
B	HOH2102

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B1159

Chain	Residue
B	ASP8
B	HIS10
B	HIS42
B	CDP1160

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN B1161

Chain	Residue
B	CDP1160
B	HOH2104
B	HOH2105
C	GLU135

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B1162

Chain	Residue
A	GLY138
A	ARG142
B	GLY138
B	ARG142
C	GLY138
C	ARG142

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C1157

Chain	Residue
A	CDP1158
C	ASP8
C	HIS10
C	HIS42

site_id	AC8
Number of Residues	21
Details	BINDING SITE FOR RESIDUE CDP A1158

Chain	Residue
A	ALA100
A	PRO103
A	LYS104
A	MSE105
A	LEU106
A	ALA131
A	THR132
A	THR133
A	GLU135
A	MN1159
A	HOH2077
A	HOH2088
A	HOH2089
A	HOH2091
A	HOH2092
C	ASP8
C	HIS10
C	HIS42
C	ASP56
C	GLY58
C	ZN1157

site_id	AC9
Number of Residues	22
Details	BINDING SITE FOR RESIDUE CDP B1157

Chain	Residue
A	ASP8
A	HIS10
A	HIS42
A	ASP56
A	GLY58
A	ZN1157
A	HOH2031
B	ALA100
B	PRO103
B	LYS104
B	MSE105
B	LEU106
B	ALA131
B	THR132
B	THR133
B	GLU135
B	MN1158
B	HOH2087
B	HOH2098
B	HOH2099
B	HOH2100
B	HOH2102

site_id	BC1
Number of Residues	20
Details	BINDING SITE FOR RESIDUE CDP B1160

Chain	Residue
B	ASP8
B	HIS10
B	HIS42
B	ASP56
B	GLY58
B	ZN1159
B	MN1161
B	HOH2037
B	HOH2103
B	HOH2104
C	ALA100
C	PRO103
C	LYS104
C	MSE105
C	LEU106
C	ALA131
C	THR132
C	THR133
C	GLU135
C	HOH2093

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	SER35-GLY50

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	9
Details	BINDING: BINDING => ECO:0000269\|PubMed:11786530, ECO:0000269\|PubMed:11829504, ECO:0000269\|PubMed:11997478, ECO:0000269\|PubMed:15608374, ECO:0000269\|PubMed:16392111, ECO:0000269\|PubMed:16511114, ECO:0000269\|PubMed:19320487, ECO:0007744\|PDB:1GX1, ECO:0007744\|PDB:1H47, ECO:0007744\|PDB:1H48, ECO:0007744\|PDB:1JY8, ECO:0007744\|PDB:1U3L, ECO:0007744\|PDB:1U3P, ECO:0007744\|PDB:1U40, ECO:0007744\|PDB:1YQN, ECO:0007744\|PDB:2AMT, ECO:0007744\|PDB:2GZL, ECO:0007744\|PDB:3ELC, ECO:0007744\|PDB:3EOR, ECO:0007744\|PDB:3ERN, ECO:0007744\|PDB:3ESJ, ECO:0007744\|PDB:3FBA

Chain	Residue	Details
A	ASP8
A	HIS10
A	HIS42
B	ASP8
B	HIS10
B	HIS42
C	ASP8
C	HIS10
C	HIS42

site_id	SWS_FT_FI2
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:11786530, ECO:0000269\|PubMed:11829504, ECO:0000269\|PubMed:15608374, ECO:0000269\|PubMed:16392111, ECO:0007744\|PDB:1H48, ECO:0007744\|PDB:1KNJ, ECO:0007744\|PDB:1U43, ECO:0007744\|PDB:2AMT

Chain	Residue	Details
A	HIS34
B	HIS34
C	HIS34

site_id	SWS_FT_FI3
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:11829504, ECO:0000269\|PubMed:11997478, ECO:0000269\|PubMed:15608374, ECO:0000269\|PubMed:16392111, ECO:0000269\|PubMed:16511114, ECO:0000269\|PubMed:19320487, ECO:0000312\|PDB:1U43, ECO:0007744\|PDB:1GX1, ECO:0007744\|PDB:1H48, ECO:0007744\|PDB:1U3L, ECO:0007744\|PDB:1U3P, ECO:0007744\|PDB:1YQN, ECO:0007744\|PDB:2AMT, ECO:0007744\|PDB:2GZL, ECO:0007744\|PDB:3ERN

Chain	Residue	Details
A	ASP56
B	ASP56
C	ASP56

site_id	SWS_FT_FI4
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:11829504, ECO:0000269\|PubMed:15608374, ECO:0000312\|PDB:1JY8, ECO:0007744\|PDB:1H48, ECO:0007744\|PDB:1U3P, ECO:0007744\|PDB:1U40

Chain	Residue	Details
A	PHE61
B	PHE61
C	PHE61

site_id	SWS_FT_FI5
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:11786530, ECO:0000269\|PubMed:11997478, ECO:0000269\|PubMed:15608374, ECO:0000269\|PubMed:16392111, ECO:0000269\|PubMed:19320487, ECO:0007744\|PDB:1GX1, ECO:0007744\|PDB:1H48, ECO:0007744\|PDB:1KNJ, ECO:0007744\|PDB:1U3L, ECO:0007744\|PDB:1YQN, ECO:0007744\|PDB:2AMT, ECO:0007744\|PDB:3ELC, ECO:0007744\|PDB:3EOR, ECO:0007744\|PDB:3ERN, ECO:0007744\|PDB:3ESJ, ECO:0007744\|PDB:3FBA

Chain	Residue	Details
A	ALA100
B	ALA100
C	ALA100

site_id	SWS_FT_FI6
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:11997478, ECO:0000269\|PubMed:15608374, ECO:0000269\|PubMed:16392111, ECO:0000269\|PubMed:19320487, ECO:0007744\|PDB:1GX1, ECO:0007744\|PDB:1H48, ECO:0007744\|PDB:1U3L, ECO:0007744\|PDB:1YQN, ECO:0007744\|PDB:2AMT, ECO:0007744\|PDB:3ERN

Chain	Residue	Details
A	THR132
B	THR132
C	THR132

site_id	SWS_FT_FI7
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:15608374, ECO:0000269\|PubMed:16392111, ECO:0000269\|PubMed:16511114, ECO:0000269\|PubMed:19320487, ECO:0007744\|PDB:1H48, ECO:0007744\|PDB:1YQN, ECO:0007744\|PDB:2AMT, ECO:0007744\|PDB:3ELC, ECO:0007744\|PDB:3ERN

Chain	Residue	Details
A	PHE139
B	PHE139
C	PHE139

site_id	SWS_FT_FI8
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:15608374, ECO:0000269\|PubMed:16392111, ECO:0000269\|PubMed:19320487, ECO:0000312\|PDB:3ELC, ECO:0007744\|PDB:1H48, ECO:0007744\|PDB:2AMT, ECO:0007744\|PDB:2GZL, ECO:0007744\|PDB:3EOR, ECO:0007744\|PDB:3ERN, ECO:0007744\|PDB:3ESJ, ECO:0007744\|PDB:3FBA

Chain	Residue	Details
A	ARG142
B	ARG142
C	ARG142

site_id	SWS_FT_FI9
Number of Residues	6
Details	SITE: Transition state stabilizer => ECO:0000255\|HAMAP-Rule:MF_00107, ECO:0000305\|PubMed:11786530

Chain	Residue	Details
A	HIS34
A	THR133
B	HIS34
B	THR133
C	HIS34
C	THR133

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