Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3T80

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine

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	4
Details	BINDING SITE FOR RESIDUE ZN A 301

Chain	Residue
A	ASP8
A	HIS10
A	HIS42
A	MG302

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 302

Chain	Residue
A	ASP8
A	HOH188
A	ZN301
C	THR132
C	HOH177

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 160

Chain	Residue
A	GLU135
B	ASP8
B	ZN301

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE CTN A 401

Chain	Residue
A	ALA100
A	PRO103
A	LYS104
A	MET105
A	LEU106
A	ALA131
A	THR133
A	EDO164
B	ASP56

site_id	AC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE POP A 161

Chain	Residue
A	GLY138
A	PHE139
A	ARG142
A	EDO162
B	GLY138
B	PHE139
B	ARG142
B	EDO161
C	GLY138
C	PHE139
C	ARG142
C	EDO160

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 162

Chain	Residue
A	PHE139
A	POP161
B	PHE139

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 164

Chain	Residue
A	GLN101
A	CTN401

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 301

Chain	Residue
A	MG160
B	ASP8
B	HIS10
B	HIS42

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG B 160

Chain	Residue
A	GLU149
B	GLU149
C	GLU149

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CTN B 401

Chain	Residue
B	ALA100
B	PRO103
B	LYS104
B	MET105
B	LEU106
B	ALA131
B	THR132
B	THR133
C	ASP56
C	GLY58

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 161

Chain	Residue
A	POP161
B	PHE139

site_id	BC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO B 162

Chain	Residue
B	GLN101

site_id	BC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO B 163

Chain	Residue
B	HIS123

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 301

Chain	Residue
C	ASP8
C	HIS10
C	HIS42
C	MG302

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 302

Chain	Residue
B	THR132
B	HOH179
B	HOH183
C	ASP8
C	ZN301

site_id	BC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE CTN C 401

Chain	Residue
A	ASP56
A	GLY58
A	LYS59
C	ALA100
C	PRO103
C	LYS104
C	MET105
C	LEU106
C	ALA131

site_id	BC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 160

Chain	Residue
A	POP161
C	PHE139

site_id	BC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 161

Chain	Residue
C	GLN101
C	LYS104

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 301

Chain	Residue
D	ASP8
D	HIS10
D	HIS42
D	HOH173
D	MG302

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 302

Chain	Residue
D	ASP8
D	HOH173
D	HOH180
D	ZN301
F	THR132

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG D 160

Chain	Residue
D	GLU149
E	GLU149
F	GLU149

site_id	CC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE CTN D 401

Chain	Residue
D	THR133
E	ASP56
E	GLY58
E	LYS59
D	ALA100
D	PRO103
D	MET105
D	LEU106
D	ALA131

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 161

Chain	Residue
D	PHE139
D	THR140
E	POP160

site_id	CC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO D 162

Chain	Residue
D	LEU137

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 301

Chain	Residue
E	ASP8
E	HIS10
E	HIS42
E	MG302

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG E 302

Chain	Residue
D	THR132
E	ASP8
E	HOH163
E	ZN301

site_id	CC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE CTN E 401

Chain	Residue
E	ALA100
E	PRO103
E	MET105
E	LEU106
E	ALA131
E	THR132
E	THR133
F	ASP56

site_id	DC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE POP E 160

Chain	Residue
D	GLY138
D	PHE139
D	ARG142
D	EDO161
E	GLY138
E	PHE139
E	ARG142
E	EDO161
F	GLY138
F	PHE139
F	ARG142
F	EDO160

site_id	DC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO E 161

Chain	Residue
E	PHE139
E	POP160

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 301

Chain	Residue
F	ASP8
F	HIS10
F	HIS42
F	MG302

site_id	DC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG F 302

Chain	Residue
E	THR132
F	ASP8
F	ZN301

site_id	DC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CTN F 401

Chain	Residue
D	ASP56
D	GLY58
D	LYS59
F	ALA100
F	PRO103
F	LYS104
F	MET105
F	LEU106
F	ALA131
F	THR132
F	THR133
F	HOH179

site_id	DC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO F 160

Chain	Residue
E	POP160
F	PHE139

site_id	DC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO F 161

Chain	Residue
E	LEU137
F	HOH171

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	60
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00107

Chain	Residue	Details
A	ASP8
A	ARG142
B	ASP8
B	HIS10
B	HIS34
B	HIS42
B	ASP56
B	PHE61
B	ALA100
B	THR132
B	PHE139
A	HIS10
B	ARG142
C	ASP8
C	HIS10
C	HIS34
C	HIS42
C	ASP56
C	PHE61
C	ALA100
C	THR132
C	PHE139
A	HIS34
C	ARG142
D	ASP8
D	HIS10
D	HIS34
D	HIS42
D	ASP56
D	PHE61
D	ALA100
D	THR132
D	PHE139
A	HIS42
D	ARG142
E	ASP8
E	HIS10
E	HIS34
E	HIS42
E	ASP56
E	PHE61
E	ALA100
E	THR132
E	PHE139
A	ASP56
E	ARG142
F	ASP8
F	HIS10
F	HIS34
F	HIS42
F	ASP56
F	PHE61
F	ALA100
F	THR132
F	PHE139
A	PHE61
F	ARG142
A	ALA100
A	THR132
A	PHE139

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

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)