3ERN

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP

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	3
Details	BINDING SITE FOR RESIDUE ZN A 800

Chain	Residue
A	ASP8
A	HIS10
A	HIS42

---

site_id	AC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CAR A 900

Chain	Residue
A	THR132
A	THR133
A	HOH927
C	ASP56
C	GLY58
C	HOH929
A	ALA100
A	PRO103
A	LYS104
A	MET105
A	LEU106
A	ALA131

---

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CAR B 900

Chain	Residue
A	ASP56
B	ALA100
B	PRO103
B	LYS104
B	MET105
B	LEU106
B	ALA131
B	THR132
B	THR133
B	HOH920
B	HOH932
B	HOH939

---

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 800

Chain	Residue
B	ASP8
B	HIS10
B	HIS42
B	SO4801

---

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 801

Chain	Residue
B	HIS10
B	HIS34
B	SER35
B	ZN800
B	HOH917
B	HOH940

---

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GPP B 901

Chain	Residue
A	GLY138
A	PHE139
A	ARG142
B	THR134
B	GLY138
B	PHE139
B	THR140
B	ARG142
C	GLY138
C	PHE139
C	ARG142
C	GLU149

---

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CAR C 900

Chain	Residue
B	ASP56
C	ALA100
C	PRO103
C	LYS104
C	MET105
C	LEU106
C	ALA131
C	THR132
C	THR133
C	HOH904

---

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN D 800

Chain	Residue
D	ASP8
D	HIS10
D	HIS42

---

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CAR D 900

Chain	Residue
D	ALA100
D	PRO103
D	LYS104
D	MET105
D	LEU106
D	ALA131
D	THR132
D	THR133
D	HOH903
D	HOH937
F	ASP56
F	GLY58

---

site_id	BC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CAR E 900

Chain	Residue
D	ASP56
D	GLY58
E	ALA100
E	PRO103
E	LYS104
E	MET105
E	LEU106
E	ALA131
E	THR132
E	THR133
E	HOH902
E	HOH916

---

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN E 800

Chain	Residue
E	ASP8
E	HIS10
E	HIS42
E	SO4801
E	HOH943

---

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 801

Chain	Residue
E	HIS10
E	ALA33
E	HIS34
E	SER35
E	HIS42
E	ZN800
E	HOH943

---

site_id	BC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GPP F 902

Chain	Residue
D	PHE139
D	ARG142
E	GLY138
E	PHE139
E	ARG142
E	GLU149
F	GLY138
F	PHE139
F	ARG142
F	GLU149
F	HOH948
D	GLY138

---

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	5
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	11
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

---