Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1IV4

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)

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	5
Details	BINDING SITE FOR RESIDUE MG A 1561

Chain	Residue
A	ASP8
A	HIS10
A	HIS42
A	MG1571
A	HOH1625

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 1562

Chain	Residue
B	HOH1630
A	MG1572
B	ASP208
B	HIS210
B	HIS242

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 1563

Chain	Residue
B	MG1573
C	ASP408
C	HIS410
C	HIS442
C	HOH1632

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 1564

Chain	Residue
D	HOH234
D	ASP1008
D	HIS1010
D	HIS1042
D	MG1574
F	HOH154

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG E 1565

Chain	Residue
D	HOH157
D	MG1575
E	ASP1208
E	HIS1210
E	HIS1242

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG F 1566

Chain	Residue
F	HOH170
F	ASP1408
F	HIS1410
F	HIS1442
F	MG1576

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG A 1571

Chain	Residue
A	ASP8
A	MG1561
A	HOH1625
A	HOH1642
C	LYS532
C	C5P1601
C	HOH1623

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG A 1572

Chain	Residue
A	LYS132
A	C5P1602
A	HOH1643
B	ASP208
B	MG1562
B	HOH1630
B	HOH1647

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG B 1573

Chain	Residue
B	LYS332
B	C5P1603
B	HOH1640
C	ASP408
C	MG1563
C	HOH1622
C	HOH1632

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG D 1574

Chain	Residue
D	HOH234
D	ASP1008
D	MG1564
F	HOH154
F	HOH416
F	LYS1532
F	C5P1604

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG D 1575

Chain	Residue
D	HOH157
D	HOH161
D	LYS1132
D	C5P1605
E	HOH204
E	ASP1208
E	MG1565

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG F 1576

Chain	Residue
E	LYS1332
F	HOH170
F	HOH176
F	HOH193
F	ASP1408
F	MG1566
F	C5P1606

site_id	BC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE C5P C 1601

Chain	Residue
A	ASP56
A	GLY58
A	MG1571
A	HOH1625
C	LEU500
C	PRO503
C	LYS504
C	LEU505
C	GLY506
C	ARG509
C	PHE531
C	LYS532
C	THR533
C	GLU535
C	HOH1614
C	HOH1623
C	HOH1667
C	HOH1682

site_id	BC5
Number of Residues	17
Details	BINDING SITE FOR RESIDUE C5P A 1602

Chain	Residue
A	THR133
A	GLU135
A	MG1572
A	HOH1640
A	HOH1643
A	HOH1692
B	ASP256
B	GLY258
B	HOH1630
A	LEU100
A	PRO103
A	LYS104
A	LEU105
A	GLY106
A	ARG109
A	PHE131
A	LYS132

site_id	BC6
Number of Residues	16
Details	BINDING SITE FOR RESIDUE C5P B 1603

Chain	Residue
B	LEU300
B	PRO303
B	LYS304
B	LEU305
B	GLY306
B	PHE331
B	LYS332
B	THR333
B	GLU335
B	MG1573
B	HOH1619
B	HOH1640
B	HOH1686
C	ASP456
C	GLY458
C	HOH1632

site_id	BC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE C5P F 1604

Chain	Residue
D	ASP1056
D	GLY1058
D	MG1574
F	HOH117
F	HOH154
F	HOH416
F	LEU1500
F	PRO1503
F	LYS1504
F	LEU1505
F	GLY1506
F	ARG1509
F	PHE1531
F	LYS1532
F	THR1533
F	GLU1535

site_id	BC8
Number of Residues	17
Details	BINDING SITE FOR RESIDUE C5P D 1605

Chain	Residue
D	HOH76
D	HOH157
D	HOH161
D	HOH383
D	HOH428
D	LEU1100
D	PRO1103
D	LYS1104
D	LEU1105
D	GLY1106
D	ARG1109
D	PHE1131
D	LYS1132
D	THR1133
D	MG1575
E	ASP1256
E	GLY1258

site_id	BC9
Number of Residues	17
Details	BINDING SITE FOR RESIDUE C5P F 1606

Chain	Residue
E	LEU1300
E	PRO1303
E	LYS1304
E	LEU1305
E	GLY1306
E	ARG1309
E	PHE1331
E	LYS1332
E	THR1333
F	HOH142
F	HOH170
F	HOH193
F	HOH397
F	ASP1456
F	ILE1457
F	GLY1458
F	MG1576

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	SER35-SER50

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	36
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00107

Chain	Residue	Details
A	ASP8
B	HIS242
B	ASP256
B	PHE261
C	ASP408
C	HIS410
C	HIS434
C	HIS442
C	ASP456
C	PHE461
D	ASP1008
A	HIS10
D	HIS1010
D	HIS1034
D	HIS1042
D	ASP1056
D	PHE1061
E	ASP1208
E	HIS1210
E	HIS1234
E	HIS1242
E	ASP1256
A	HIS34
E	PHE1261
F	ASP1408
F	HIS1410
F	HIS1434
F	HIS1442
F	ASP1456
F	PHE1461
A	HIS42
A	ASP56
A	PHE61
B	ASP208
B	HIS210
B	HIS234

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING:

Chain	Residue	Details
A	LEU100
E	PHE1331
F	LEU1500
F	PHE1531
A	PHE131
B	LEU300
B	PHE331
C	LEU500
C	PHE531
D	LEU1100
D	PHE1131
E	LEU1300

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

Chain	Residue	Details
A	HIS34
E	THR1333
F	HIS1434
F	THR1533
A	THR133
B	HIS234
B	THR333
C	HIS434
C	THR533
D	HIS1034
D	THR1133
E	HIS1234

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)