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Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase with cmp
Analyse Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F0G
- Type
- protein
- Length
- 917 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- EC
- 4.6.1.12
- UniProt
- Q63T71
- Ligands
- C5P, ZN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 159 | 33% helix, 33% strand | Q63T71 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 154 | 34% helix, 30% strand | Q63T71 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 149 | 36% helix, 31% strand | Q63T71 |
| E | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 148 | 33% helix, 35% strand | Q63T71 |
| F | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 148 | 36% helix, 32% strand | Q63T71 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 5 copies · chains A, B, C, D, F, E
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.83 | 0.95 | 46 | empty |
| 2 | 248 | 0.82 | 0.94 | 45 | empty |
| 3 | 280 | 0.63 | 0.81 | 36 | C5P |
| 4 | 261 | 0.62 | 0.81 | 40 | C5P |
| 5 | 240 | 0.51 | 0.75 | 29 | C5P |
Interfaces
6 interfaces between chains.
- E–F · 1218 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1211 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1180 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1153 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1140 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3F0G · Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase with CMP · the same entry in another collection · chain F against F, TM-score 1.00
- Q63T71 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain F against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q63T71
- Elsewhere: RCSB PDB 3F0G · PDBe 3F0G · UniProt Q63T71
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