Research workbench
Crystal structure of tRNA modification enzyme miaa in the complex with TRNA(PHE)
Analyse Crystal structure of tRNA modification enzyme miaa in the complex with TRNA(PHE) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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