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 | 18 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11786530, ECO:0000269|PubMed:11829504, ECO:0000269|PubMed:11997478, ECO:0000269|PubMed:15608374, ECO:0000269|PubMed:16392111, ECO:0000269|PubMed:16511114, ECO:0000269|PubMed:19320487, ECO:0007744|PDB:1GX1, ECO:0007744|PDB:1H47, ECO:0007744|PDB:1H48, ECO:0007744|PDB:1JY8, ECO:0007744|PDB:1U3L, ECO:0007744|PDB:1U3P, ECO:0007744|PDB:1U40, ECO:0007744|PDB:1YQN, ECO:0007744|PDB:2AMT, ECO:0007744|PDB:2GZL, ECO:0007744|PDB:3ELC, ECO:0007744|PDB:3EOR, ECO:0007744|PDB:3ERN, ECO:0007744|PDB:3ESJ, ECO:0007744|PDB:3FBA |
Chain | Residue | Details |
A | ASP8 | |
D | ASP8 | |
D | HIS10 | |
D | HIS42 | |
E | ASP8 | |
E | HIS10 | |
E | HIS42 | |
F | ASP8 | |
F | HIS10 | |
F | HIS42 | |
A | HIS10 | |
A | HIS42 | |
B | ASP8 | |
B | HIS10 | |
B | HIS42 | |
C | ASP8 | |
C | HIS10 | |
C | HIS42 |
site_id | SWS_FT_FI2 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11786530, ECO:0000269|PubMed:11829504, ECO:0000269|PubMed:15608374, ECO:0000269|PubMed:16392111, ECO:0007744|PDB:1H48, ECO:0007744|PDB:1KNJ, ECO:0007744|PDB:1U43, ECO:0007744|PDB:2AMT |
Chain | Residue | Details |
A | HIS34 | |
B | HIS34 | |
C | HIS34 | |
D | HIS34 | |
E | HIS34 | |
F | HIS34 |
site_id | SWS_FT_FI3 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11829504, ECO:0000269|PubMed:11997478, ECO:0000269|PubMed:15608374, ECO:0000269|PubMed:16392111, ECO:0000269|PubMed:16511114, ECO:0000269|PubMed:19320487, ECO:0000312|PDB:1U43, ECO:0007744|PDB:1GX1, ECO:0007744|PDB:1H48, ECO:0007744|PDB:1U3L, ECO:0007744|PDB:1U3P, ECO:0007744|PDB:1YQN, ECO:0007744|PDB:2AMT, ECO:0007744|PDB:2GZL, ECO:0007744|PDB:3ERN |
Chain | Residue | Details |
A | ASP56 | |
B | ASP56 | |
C | ASP56 | |
D | ASP56 | |
E | ASP56 | |
F | ASP56 |
site_id | SWS_FT_FI4 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11829504, ECO:0000269|PubMed:15608374, ECO:0000312|PDB:1JY8, ECO:0007744|PDB:1H48, ECO:0007744|PDB:1U3P, ECO:0007744|PDB:1U40 |
Chain | Residue | Details |
A | PHE61 | |
B | PHE61 | |
C | PHE61 | |
D | PHE61 | |
E | PHE61 | |
F | PHE61 |
site_id | SWS_FT_FI5 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11786530, ECO:0000269|PubMed:11997478, ECO:0000269|PubMed:15608374, ECO:0000269|PubMed:16392111, ECO:0000269|PubMed:19320487, ECO:0007744|PDB:1GX1, ECO:0007744|PDB:1H48, ECO:0007744|PDB:1KNJ, ECO:0007744|PDB:1U3L, ECO:0007744|PDB:1YQN, ECO:0007744|PDB:2AMT, ECO:0007744|PDB:3ELC, ECO:0007744|PDB:3EOR, ECO:0007744|PDB:3ERN, ECO:0007744|PDB:3ESJ, ECO:0007744|PDB:3FBA |
Chain | Residue | Details |
A | ALA100 | |
B | ALA100 | |
C | ALA100 | |
D | ALA100 | |
E | ALA100 | |
F | ALA100 |
site_id | SWS_FT_FI6 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11997478, ECO:0000269|PubMed:15608374, ECO:0000269|PubMed:16392111, ECO:0000269|PubMed:19320487, ECO:0007744|PDB:1GX1, ECO:0007744|PDB:1H48, ECO:0007744|PDB:1U3L, ECO:0007744|PDB:1YQN, ECO:0007744|PDB:2AMT, ECO:0007744|PDB:3ERN |
Chain | Residue | Details |
A | THR132 | |
B | THR132 | |
C | THR132 | |
D | THR132 | |
E | THR132 | |
F | THR132 |
site_id | SWS_FT_FI7 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15608374, ECO:0000269|PubMed:16392111, ECO:0000269|PubMed:16511114, ECO:0000269|PubMed:19320487, ECO:0007744|PDB:1H48, ECO:0007744|PDB:1YQN, ECO:0007744|PDB:2AMT, ECO:0007744|PDB:3ELC, ECO:0007744|PDB:3ERN |
Chain | Residue | Details |
A | PHE139 | |
B | PHE139 | |
C | PHE139 | |
D | PHE139 | |
E | PHE139 | |
F | PHE139 |
site_id | SWS_FT_FI8 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15608374, ECO:0000269|PubMed:16392111, ECO:0000269|PubMed:19320487, ECO:0000312|PDB:3ELC, ECO:0007744|PDB:1H48, ECO:0007744|PDB:2AMT, ECO:0007744|PDB:2GZL, ECO:0007744|PDB:3EOR, ECO:0007744|PDB:3ERN, ECO:0007744|PDB:3ESJ, ECO:0007744|PDB:3FBA |
Chain | Residue | Details |
A | ARG142 | |
B | ARG142 | |
C | ARG142 | |
D | ARG142 | |
E | ARG142 | |
F | ARG142 |
site_id | SWS_FT_FI9 |
Number of Residues | 12 |
Details | SITE: Transition state stabilizer => ECO:0000255|HAMAP-Rule:MF_00107, ECO:0000305|PubMed:11786530 |
Chain | Residue | Details |
A | HIS34 | |
E | THR133 | |
F | HIS34 | |
F | THR133 | |
A | THR133 | |
B | HIS34 | |
B | THR133 | |
C | HIS34 | |
C | THR133 | |
D | HIS34 | |
D | THR133 | |
E | HIS34 |