Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3ERN

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP

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
D	0005515	molecular_function	protein binding
D	0006744	biological_process	ubiquinone biosynthetic process
D	0008270	molecular_function	zinc 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	0030145	molecular_function	manganese ion binding
D	0042802	molecular_function	identical protein binding
D	0046872	molecular_function	metal ion binding
E	0005515	molecular_function	protein binding
E	0006744	biological_process	ubiquinone biosynthetic process
E	0008270	molecular_function	zinc 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	0030145	molecular_function	manganese ion binding
E	0042802	molecular_function	identical protein binding
E	0046872	molecular_function	metal ion binding
F	0005515	molecular_function	protein binding
F	0006744	biological_process	ubiquinone biosynthetic process
F	0008270	molecular_function	zinc 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	0030145	molecular_function	manganese ion binding
F	0042802	molecular_function	identical protein binding
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN A 800

Chain	Residue
A	ASP8
A	HIS10
A	HIS42

site_id	AC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CAR A 900

Chain	Residue
A	THR132
A	THR133
A	HOH927
C	ASP56
C	GLY58
C	HOH929
A	ALA100
A	PRO103
A	LYS104
A	MET105
A	LEU106
A	ALA131

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CAR B 900

Chain	Residue
A	ASP56
B	ALA100
B	PRO103
B	LYS104
B	MET105
B	LEU106
B	ALA131
B	THR132
B	THR133
B	HOH920
B	HOH932
B	HOH939

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 800

Chain	Residue
B	ASP8
B	HIS10
B	HIS42
B	SO4801

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 801

Chain	Residue
B	HIS10
B	HIS34
B	SER35
B	ZN800
B	HOH917
B	HOH940

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GPP B 901

Chain	Residue
A	GLY138
A	PHE139
A	ARG142
B	THR134
B	GLY138
B	PHE139
B	THR140
B	ARG142
C	GLY138
C	PHE139
C	ARG142
C	GLU149

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CAR C 900

Chain	Residue
B	ASP56
C	ALA100
C	PRO103
C	LYS104
C	MET105
C	LEU106
C	ALA131
C	THR132
C	THR133
C	HOH904

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN D 800

Chain	Residue
D	ASP8
D	HIS10
D	HIS42

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CAR D 900

Chain	Residue
D	ALA100
D	PRO103
D	LYS104
D	MET105
D	LEU106
D	ALA131
D	THR132
D	THR133
D	HOH903
D	HOH937
F	ASP56
F	GLY58

site_id	BC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CAR E 900

Chain	Residue
D	ASP56
D	GLY58
E	ALA100
E	PRO103
E	LYS104
E	MET105
E	LEU106
E	ALA131
E	THR132
E	THR133
E	HOH902
E	HOH916

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN E 800

Chain	Residue
E	ASP8
E	HIS10
E	HIS42
E	SO4801
E	HOH943

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 801

Chain	Residue
E	HIS10
E	ALA33
E	HIS34
E	SER35
E	HIS42
E	ZN800
E	HOH943

site_id	BC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GPP F 902

Chain	Residue
D	PHE139
D	ARG142
E	GLY138
E	PHE139
E	ARG142
E	GLU149
F	GLY138
F	PHE139
F	ARG142
F	GLU149
F	HOH948
D	GLY138

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	18
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
D	ASP8
D	HIS10
D	HIS42
E	ASP8
E	HIS10
E	HIS42
F	ASP8
F	HIS10
F	HIS42
A	HIS10
A	HIS42
B	ASP8
B	HIS10
B	HIS42
C	ASP8
C	HIS10
C	HIS42

site_id	SWS_FT_FI2
Number of Residues	6
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
D	HIS34
E	HIS34
F	HIS34

site_id	SWS_FT_FI3
Number of Residues	6
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
D	ASP56
E	ASP56
F	ASP56

site_id	SWS_FT_FI4
Number of Residues	6
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
D	PHE61
E	PHE61
F	PHE61

site_id	SWS_FT_FI5
Number of Residues	6
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
D	ALA100
E	ALA100
F	ALA100

site_id	SWS_FT_FI6
Number of Residues	6
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
D	THR132
E	THR132
F	THR132

site_id	SWS_FT_FI7
Number of Residues	6
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
D	PHE139
E	PHE139
F	PHE139

site_id	SWS_FT_FI8
Number of Residues	6
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
D	ARG142
E	ARG142
F	ARG142

site_id	SWS_FT_FI9
Number of Residues	12
Details	SITE: Transition state stabilizer => ECO:0000255\|HAMAP-Rule:MF_00107, ECO:0000305\|PubMed:11786530

Chain	Residue	Details
A	HIS34
E	THR133
F	HIS34
F	THR133
A	THR133
B	HIS34
B	THR133
C	HIS34
C	THR133
D	HIS34
D	THR133
E	HIS34

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