3ELC
Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand
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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ZN A 801 |
| Chain | Residue |
| A | ASP8 |
| A | HIS10 |
| A | HIS42 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE F01 A 901 |
| Chain | Residue |
| A | THR132 |
| A | THR133 |
| C | ASP56 |
| C | GLY58 |
| A | ALA100 |
| A | PRO103 |
| A | LYS104 |
| A | MET105 |
| A | LEU106 |
| A | ALA131 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ZN B 802 |
| Chain | Residue |
| B | ASP8 |
| B | HIS10 |
| B | HIS42 |
| site_id | AC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE F01 B 902 |
| Chain | Residue |
| A | ASP56 |
| A | GLY58 |
| B | ALA100 |
| B | PRO103 |
| B | LYS104 |
| B | MET105 |
| B | LEU106 |
| B | ALA131 |
| B | THR132 |
| B | THR133 |
| B | HOH929 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ZN C 803 |
| Chain | Residue |
| C | ASP8 |
| C | HIS10 |
| C | HIS42 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE F01 C 903 |
| Chain | Residue |
| B | ASP56 |
| B | GLY58 |
| C | ALA100 |
| C | PRO103 |
| C | LYS104 |
| C | MET105 |
| C | LEU106 |
| C | ALA131 |
| C | THR132 |
| C | THR133 |
| site_id | AC7 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GPP C 904 |
| Chain | Residue |
| A | GLY138 |
| A | PHE139 |
| A | ARG142 |
| B | GLY138 |
| B | PHE139 |
| B | ARG142 |
| C | THR134 |
| C | GLY138 |
| C | PHE139 |
| C | ARG142 |
| C | HOH928 |
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 | 9 |
| 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 | |
| A | HIS10 | |
| A | HIS42 | |
| B | ASP8 | |
| B | HIS10 | |
| B | HIS42 | |
| C | ASP8 | |
| C | HIS10 | |
| C | HIS42 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | SITE: Transition state stabilizer => ECO:0000255|HAMAP-Rule:MF_00107, ECO:0000305|PubMed:11786530 |
| Chain | Residue | Details |
| A | HIS34 | |
| A | THR133 | |
| B | HIS34 | |
| B | THR133 | |
| C | HIS34 | |
| C | THR133 |
