MolNFT v1 · #56654 · protein + RNA
Crystal structure of tRNA modification enzyme miaa in the complex with TRNA(PHE)
2ZM5 · TRNA DELTA(2)-isopentenylpyrophosphate transferase: “Crystal structure of tRNA modification enzyme miaa in the complex with TRNA(PHE)”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability 0.65). MolNFT v1 #56654 on…
- PDB
- 2ZM5
- Type
- protein + RNA
- Length
- 754 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA DELTA(2)-isopentenylpyrophosphate transferase; TRNA(PHE)
- EC
- 2.5.1.8
- UniProt
- P16384
- Ligands
- MG
- Pockets
- 16 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 306 | 53% helix, 11% strand | P16384 |
| B | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 305 | 48% helix, 11% strand | P16384 |
| C | TRNA(PHE) | rna | 74 | — | — |
| D | TRNA(PHE) | rna | 69 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.65 | 0.85 | 38 | empty |
| 2 | 562 | 0.65 | 0.77 | 31 | MG |
| 3 | 524 | 0.63 | 0.77 | 32 | MG |
| 4 | 377 | 0.63 | 0.79 | 50 | empty |
| 5 | 464 | 0.62 | 0.77 | 30 | MG |
Interfaces
5 interfaces between chains.
- A–C · 2007 Ų buried · 54 hydrogen bonds · protein-nucleic
- B–D · 1993 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–B · 426 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 266 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 50 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2ZM5 · Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) · the same entry in another collection · chain A against A, TM-score 1.00
- P16384 · AlphaFold monomer V2.0 prediction for tRNA dimethylallyltransferase (P16384) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P16384
- Elsewhere: RCSB PDB 2ZM5 · PDBe 2ZM5 · UniProt P16384
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.