Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5IWY

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+

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	6
Details	binding site for residue MG A 201

Chain	Residue
A	ASP9
A	HIS11
A	HIS43
A	HOH319
A	HOH331
A	HOH357

site_id	AC2
Number of Residues	17
Details	binding site for residue C5P A 202

Chain	Residue
A	MET106
A	LEU107
A	ALA132
A	THR133
A	THR134
A	GLU136
A	HOH302
A	HOH304
A	HOH314
A	HOH342
C	ASP57
C	GLY59
C	HOH302
C	HOH331
A	ALA101
A	PRO104
A	LYS105

site_id	AC3
Number of Residues	13
Details	binding site for residue C5P B 201

Chain	Residue
A	ASP57
A	GLY59
A	HOH301
A	HOH319
B	ALA101
B	PRO104
B	LYS105
B	MET106
B	LEU107
B	ALA132
B	THR133
B	THR134
B	HOH304

site_id	AC4
Number of Residues	6
Details	binding site for residue MG B 202

Chain	Residue
B	ASP9
B	HIS11
B	HIS43
B	HOH307
B	HOH328
B	HOH341

site_id	AC5
Number of Residues	14
Details	binding site for residue C5P C 201

Chain	Residue
B	ASP57
B	GLY59
B	HOH307
B	HOH312
B	HOH330
C	ALA101
C	PRO104
C	LYS105
C	MET106
C	LEU107
C	ALA132
C	THR133
C	THR134
C	HOH301

site_id	AC6
Number of Residues	5
Details	binding site for residue MG C 202

Chain	Residue
C	ASP9
C	HIS11
C	HIS43
C	HOH324
C	HOH331

site_id	AC7
Number of Residues	6
Details	binding site for residue MG D 201

Chain	Residue
D	ASP9
D	HIS11
D	HIS43
D	HOH308
D	HOH332
D	HOH339

site_id	AC8
Number of Residues	6
Details	binding site for residue MG E 201

Chain	Residue
E	ASP9
E	HIS11
E	HIS43
E	HOH302
E	HOH323
E	HOH324

site_id	AC9
Number of Residues	12
Details	binding site for residue C5P F 201

Chain	Residue
E	ASP57
F	ALA101
F	PRO104
F	LYS105
F	MET106
F	LEU107
F	ALA132
F	THR133
F	THR134
F	GLU136
F	HOH303
F	HOH307

site_id	AD1
Number of Residues	6
Details	binding site for residue MG F 202

Chain	Residue
F	ASP9
F	HIS11
F	HIS43
F	HOH310
F	HOH331
F	HOH332

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	SER36-GLY51

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	ASP9
A	ARG143
B	ASP9
B	HIS11
B	HIS35
B	HIS43
B	ASP57
B	PHE62
B	ALA101
B	THR133
B	PHE140
A	HIS11
B	ARG143
C	ASP9
C	HIS11
C	HIS35
C	HIS43
C	ASP57
C	PHE62
C	ALA101
C	THR133
C	PHE140
A	HIS35
C	ARG143
D	ASP9
D	HIS11
D	HIS35
D	HIS43
D	ASP57
D	PHE62
D	ALA101
D	THR133
D	PHE140
A	HIS43
D	ARG143
E	ASP9
E	HIS11
E	HIS35
E	HIS43
E	ASP57
E	PHE62
E	ALA101
E	THR133
E	PHE140
A	ASP57
E	ARG143
F	ASP9
F	HIS11
F	HIS35
F	HIS43
F	ASP57
F	PHE62
F	ALA101
F	THR133
F	PHE140
A	PHE62
F	ARG143
A	ALA101
A	THR133
A	PHE140

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

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

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