MolNFT v1 · #62773 · protein + RNA
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism
3EPH · TRNA isopentenyltransferase: “Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA…”. X-ray diffraction, 3 ligands (PPV, MG, ZN), 13 pockets (best druggability 0.88). MolNFT v1 #62773…
- PDB
- 3EPH
- 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
- PPV, MG, ZN
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA isopentenyltransferase (EC 2.5.1.8) | protein | 402 | 51% helix, 12% strand | P07884 |
| E, F | TRNA | rna | 69 | — | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 10 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
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.88 | 0.90 | 111 | empty |
| 2 | 856 | 0.76 | 0.80 | 72 | MG |
| 3 | 831 | 0.74 | 0.79 | 49 | empty |
| 4 | 50 | 0.70 | 0.99 | 14 | empty |
| 5 | 254 | 0.66 | 0.83 | 41 | MG, PPV |
Interfaces
3 interfaces between chains.
- A–E · 2451 Ų buried · 71 hydrogen bonds · protein-nucleic
- B–F · 2399 Ų buried · 66 hydrogen bonds · protein-nucleic
- A–B · 1247 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3EPH · 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 3EPH · PDBe 3EPH · UniProt P07884
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