Research workbench
Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase
Analyse Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VGW
- Type
- protein
- Length
- 1,273 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-diphosphocytidyl-2C-methyl-D-erythritol synthase
- EC
- 2.7.7.-
- UniProt
- Q5F829
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (EC 2.7.7.-) | protein | 212 | 32% helix, 25% strand | Q5F829 |
| B | 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (EC 2.7.7.-) | protein | 214 | 32% helix, 24% strand | Q5F829 |
| C | 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (EC 2.7.7.-) | protein | 214 | 31% helix, 24% strand | Q5F829 |
| D | 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (EC 2.7.7.-) | protein | 211 | 33% helix, 26% strand | Q5F829 |
| E | 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (EC 2.7.7.-) | protein | 213 | 31% helix, 25% strand | Q5F829 |
| F | 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (EC 2.7.7.-) | protein | 209 | 31% helix, 25% strand | Q5F829 |
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.80 | 0.82 | 92 | empty |
| 2 | 703 | 0.78 | 0.83 | 67 | empty |
| 3 | 749 | 0.77 | 0.82 | 71 | empty |
| 4 | 155 | 0.47 | 0.77 | 23 | empty |
| 5 | 119 | 0.44 | 0.78 | 23 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2074 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2066 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1946 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 663 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 476 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1VGW · Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase · the same entry in another collection · chain F against F, TM-score 1.00
- Q5F829 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 4-phosphate… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q5F829
- Elsewhere: RCSB PDB 1VGW · PDBe 1VGW · UniProt Q5F829
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