1H48

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product

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	4
Details	BINDING SITE FOR RESIDUE ZN A 900

Chain	Residue
A	ASP8
A	HIS10
A	HIS42
A	CDI201

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 900

Chain	Residue
B	ASP8
B	HIS10
B	HIS42
B	CDI902

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 900

Chain	Residue
C	HIS10
C	HIS42
C	CDI902
C	ASP8

---

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN C 902

Chain	Residue
A	HIS5
A	GLU149
B	GLU149
C	HIS5
C	GLU149
C	HOH1001

---

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 900

Chain	Residue
D	ASP8
D	HIS10
D	HIS42
D	CDI201

---

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MN D 902

Chain	Residue
D	HIS5
D	GLU149
D	HOH301
E	HIS5
E	GLU149
F	HIS5
F	GLU149

---

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 900

Chain	Residue
E	ASP8
E	HIS10
E	HIS42
E	CDI902

---

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 900

Chain	Residue
F	ASP8
F	HIS10
F	HIS42
F	CDI902

---

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CDI A 421

Chain	Residue
A	ASP8
A	HIS10
A	ALA33
A	HIS34
A	SER35
A	HIS42
A	ILE57
A	PHE61
A	ASP63
A	ZN202
B	C5P901
B	GLU135

---

site_id	BC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE C5P A 901

Chain	Residue
A	ASP56
A	GLY58
A	CDI201
A	HOH308
B	ALA100
B	PRO103
B	LYS104
B	MET105
B	LEU106
B	ALA131
B	THR132
B	THR133
B	GLU135

---

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CDI B 421

Chain	Residue
B	ASP8
B	HIS10
B	HIS34
B	SER35
B	HIS42
B	ILE57
B	PHE61
B	ZN903
C	C5P901
C	GLU135

---

site_id	BC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE C5P B 901

Chain	Residue
B	ASP56
B	GLY58
B	ASP63
B	CDI902
B	HOH1001
C	ALA100
C	PRO103
C	LYS104
C	MET105
C	LEU106
C	ALA131
C	THR132
C	THR133

---

site_id	BC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE CDI C 421

Chain	Residue
A	HOH301
A	GLU135
C	ASP8
C	HIS10
C	ALA33
C	HIS34
C	SER35
C	HIS42
C	ILE57
C	GLY58
C	PHE61
C	ASP63
C	ZN903
A	C5P203
C	HOH1004

---

site_id	BC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE C5P C 901

Chain	Residue
A	ALA100
A	PRO103
A	LYS104
A	MET105
A	LEU106
A	ALA131
A	THR132
A	THR133
A	GLU135
C	ASP56
C	GLY58
C	LYS59
C	ASP63
C	CDI902
C	HOH1004
A	HOH301

---

site_id	BC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE CDI D 421

Chain	Residue
D	ASP8
D	HIS10
D	HIS34
D	SER35
D	HIS42
D	ILE57
D	GLY58
D	PHE61
D	ASP63
D	ZN202
E	C5P901

---

site_id	BC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE C5P D 901

Chain	Residue
D	GLY58
D	ASP63
D	CDI201
E	ALA100
E	PRO103
E	LYS104
E	MET105
E	LEU106
E	ALA131
E	THR132
E	THR133
E	GLU135

---

site_id	BC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CDI E 421

Chain	Residue
E	ASP8
E	HIS10
E	HIS34
E	SER35
E	HIS42
E	ILE57
E	PHE61
E	PRO62
E	ASP63
E	ZN903
F	C5P901
F	GLU135

---

site_id	BC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE C5P E 901

Chain	Residue
E	ASP56
E	GLY58
E	LYS59
E	CDI902
F	ALA100
F	PRO103
F	LYS104
F	MET105
F	LEU106
F	ALA131
F	THR132
F	THR133

---

site_id	CC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE CDI F 421

Chain	Residue
D	GLU135
F	ASP8
F	HIS10
F	ALA33
F	HIS34
F	SER35
F	HIS42
F	ILE57
F	GLY58
F	PHE61
F	ASP63
F	ZN903
D	C5P204

---

site_id	CC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE C5P F 901

Chain	Residue
D	ALA100
D	PRO103
D	LYS104
D	MET105
D	LEU106
D	ALA131
D	THR132
D	THR133
D	GLU135
F	ASP56
F	GLY58
F	CDI902

---

site_id	CC3
Number of Residues	18
Details	BINDING SITE FOR RESIDUE GPP G 903

Chain	Residue
A	PHE7
A	GLY138
A	PHE139
A	THR140
A	ARG142
A	GLU149
B	PHE7
B	GLY138
B	PHE139
B	THR140
B	ARG142
C	PHE7
C	GLY138
C	PHE139
C	THR140
C	ARG142
C	GLU149
C	HOH1001

---

site_id	CC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE GPP H 903

Chain	Residue
D	PHE7
D	THR134
D	GLY138
D	PHE139
D	THR140
D	ARG142
D	HOH301
E	PHE7
E	GLY138
E	PHE139
E	THR140
E	ARG142
E	GLU149
F	GLY138
F	PHE139
F	THR140
F	ARG142
F	GLU149

---

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	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16511114","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1U3P","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1JY8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U40","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11786530","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16511114","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H47","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1JY8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U40","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ELC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ESJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FBA","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11786530","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KNJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U43","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16511114","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1U43","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1JY8","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U40","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11786530","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KNJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ELC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ESJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FBA","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16511114","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ELC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3ELC","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ESJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FBA","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	12
Details	Site: {"description":"Transition state stabilizer","evidences":[{"source":"HAMAP-Rule","id":"MF_00107","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11786530","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---