MolNFT v1 · #25140 · protein
Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase
1VGT · 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: “Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase”. X-ray diffraction, 2 pockets (best druggability 0.76). MolNFT v1 #25140 on GenesisL1: 3D structure…
- PDB
- 1VGT
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
- EC
- 2.7.7.60
- UniProt
- Q46893
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 207 | 35% helix, 28% strand | Q46893 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 217 | 32% helix, 27% strand | Q46893 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.76 | 0.80 | 68 | empty |
| 2 | 226 | 0.54 | 0.78 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1703 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1VGT · Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase · the same entry in another collection · chain A against A, TM-score 1.00
- Q46893 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 4-phosphate… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q46893
- Elsewhere: RCSB PDB 1VGT · PDBe 1VGT · UniProt Q46893
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