Research workbench
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism
Analyse Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EPL
- Type
- protein + RNA
- Length
- 942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA isopentenyltransferase; TRNA
- EC
- 2.5.1.8
- UniProt
- P07884
- Ligands
- DMA, MG, ZN
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA isopentenyltransferase (EC 2.5.1.8) | protein | 402 | 51% helix, 9% strand | P07884 |
| E | TRNA | rna | 69 | — | — |
| F | TRNA | rna | 69 | — | — |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains E, B, F
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.87 | 0.89 | 105 | empty |
| 2 | 886 | 0.77 | 0.81 | 62 | empty |
| 3 | 944 | 0.75 | 0.79 | 67 | MG |
| 4 | 213 | 0.73 | 0.89 | 24 | empty |
| 5 | 76 | 0.72 | 0.97 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–E · 2500 Ų buried · 59 hydrogen bonds · protein-nucleic
- B–F · 2350 Ų buried · 57 hydrogen bonds · protein-nucleic
- A–B · 1122 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3EPL · Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight… · the same entry in another collection · chain A against A, TM-score 1.00
- P07884 · AlphaFold monomer V2.0 prediction for tRNA dimethylallyltransferase (P07884) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P07884
- Elsewhere: RCSB PDB 3EPL · PDBe 3EPL · UniProt P07884
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