MolNFT v1 · #25362 · protein
Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393) from thermotoga maritima at 2.67 a resolution
1VPA: “Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393) from thermotoga…”. X-ray diffraction, 2 ligands (CTP, MG), 3 pockets (best druggability 0.69). MolNFT v1 #25362 on GenesisL1: 3D structure…
- PDB
- 1VPA
- Type
- protein
- Length
- 441 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
- Q9X1B3
- Ligands
- CTP, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 221 | 36% helix, 28% strand | Q9X1B3 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 220 | 35% helix, 27% strand | Q9X1B3 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.69 | 0.94 | 28 | empty |
| 2 | 357 | 0.66 | 0.80 | 41 | MG, CTP, ACY |
| 3 | 326 | 0.65 | 0.81 | 43 | MG, CTP, ACY |
Interfaces
1 interface between chains.
- A–B · 2201 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 1VPA · Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1B3 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 4-phosphate… · a predicted model of the same protein · chain A 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 Q9X1B3
- Elsewhere: RCSB PDB 1VPA · PDBe 1VPA · UniProt Q9X1B3
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