Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3F0G

Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase with CMP

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	15
Details	BINDING SITE FOR RESIDUE C5P E 163

Chain	Residue
D	ASP58
E	THR135
E	HOH273
E	HOH439
E	HOH487
E	HOH523
E	HOH524
D	GLY60
E	ALA102
E	PRO105
E	LYS106
E	LEU107
E	ALA108
E	ALA133
E	LYS134

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE C5P C 163

Chain	Residue
B	ASP58
B	GLY60
C	ALA102
C	PRO105
C	LYS106
C	LEU107
C	ALA108
C	ALA133
C	LYS134
C	THR135
C	GLU137
C	HOH550
C	HOH552

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE C5P F 163

Chain	Residue
E	ASP58
E	GLY60
F	ALA102
F	PRO105
F	LYS106
F	LEU107
F	ALA108
F	ALA133
F	LYS134
F	THR135
F	HOH554
F	HOH555

site_id	AC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE C5P D 163

Chain	Residue
D	ALA102
D	PRO105
D	LYS106
D	LEU107
D	ALA108
D	ALA133
D	LYS134
D	THR135
D	GLU137
D	HOH354
F	ASP58
F	GLY60

site_id	AC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE C5P B 163

Chain	Residue
A	ASP58
A	GLY60
A	ASP65
B	ALA102
B	PRO105
B	LYS106
B	LEU107
B	ALA108
B	ALA133
B	LYS134
B	THR135
B	GLU137

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 163

Chain	Residue
A	ASP10
A	HIS12
A	HIS44
B	HOH197

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 164

Chain	Residue
D	ASP10
D	HIS12
D	HIS44
E	HOH180

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 164

Chain	Residue
D	HOH170
F	ASP10
F	HIS12
F	HIS44

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 164

Chain	Residue
E	ASP10
E	HIS12
E	HIS44
F	HOH427

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN B 164

Chain	Residue
B	ASP10
B	HIS12
B	HIS44

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 164

Chain	Residue
C	ASP10
C	HIS12
C	HIS44
C	HOH424

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	SER37-GLY52

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	42
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00107

Chain	Residue	Details
A	ASP10
B	HIS36
B	HIS44
B	ASP58
B	PHE63
B	ARG144
C	ASP10
C	HIS12
C	HIS36
C	HIS44
C	ASP58
A	HIS12
C	PHE63
C	ARG144
D	ASP10
D	HIS12
D	HIS36
D	HIS44
D	ASP58
D	PHE63
D	ARG144
E	ASP10
A	HIS36
E	HIS12
E	HIS36
E	HIS44
E	ASP58
E	PHE63
E	ARG144
F	ASP10
F	HIS12
F	HIS36
F	HIS44
A	HIS44
F	ASP58
F	PHE63
F	ARG144
A	ASP58
A	PHE63
A	ARG144
B	ASP10
B	HIS12

site_id	SWS_FT_FI2
Number of Residues	24
Details	BINDING:

Chain	Residue	Details
A	ASP67
D	ASP67
D	ALA102
D	ALA133
E	ASP67
E	ALA102
E	ALA133
F	ASP67
F	ALA102
F	ALA133
A	ASP40
A	ALA102
B	ASP40
C	ASP40
D	ASP40
E	ASP40
F	ASP40
A	ALA133
B	ASP67
B	ALA102
B	ALA133
C	ASP67
C	ALA102
C	ALA133

site_id	SWS_FT_FI3
Number of Residues	12
Details	SITE: Transition state stabilizer => ECO:0000255\|HAMAP-Rule:MF_00107

Chain	Residue	Details
A	HIS36
E	THR135
F	HIS36
F	THR135
A	THR135
B	HIS36
B	THR135
C	HIS36
C	THR135
D	HIS36
D	THR135
E	HIS36

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