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
- 3EPK
- 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
- DST, PPV, MG, ZN
- Pockets
- 16 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA isopentenyltransferase (EC 2.5.1.8) | protein | 402 | 49% helix, 12% strand | P07884 |
| E, F | TRNA | rna | 69 | — | — |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · chains A, E
- PPV · Pyrophosphate · ligand · chains B
- MG · Magnesium ion · metal · 14 copies · chains A, 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
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.89 | 0.90 | 111 | empty |
| 2 | 803 | 0.76 | 0.81 | 62 | MG |
| 3 | 810 | 0.72 | 0.78 | 48 | MG |
| 4 | 52 | 0.71 | 0.99 | 14 | empty |
| 5 | 53 | 0.71 | 0.99 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–E · 2459 Ų buried · 67 hydrogen bonds · protein-nucleic
- B–F · 2424 Ų buried · 64 hydrogen bonds · protein-nucleic
- A–B · 1234 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3EPK · 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 0.95
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 3EPK · PDBe 3EPK · UniProt P07884
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