MolNFT v1 · #57020 · protein + RNA
Crystal structure of tRNA modification enzyme miaa in the complex with TRNA(PHE) and dmaspp
2ZXU · TRNA DELTA(2)-isopentenylpyrophosphate transferase: “Crystal structure of tRNA modification enzyme miaa in the complex with TRNA(PHE) and dmaspp”. X-ray diffraction, 2 ligands (DST, MG), 17 pockets (best druggability 0.69). MolNFT…
- PDB
- 2ZXU
- 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
- DST, MG
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 306 | 51% helix, 11% strand | P16384 |
| B | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 305 | 47% helix, 11% strand | P16384 |
| C | TRNA(PHE) | rna | 74 | — | — |
| D | TRNA(PHE) | rna | 69 | — | — |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.69 | 0.87 | 38 | DST, MG |
| 2 | 345 | 0.68 | 0.82 | 53 | DST, MG |
| 3 | 552 | 0.64 | 0.77 | 31 | MG |
| 4 | 525 | 0.64 | 0.77 | 36 | MG |
| 5 | 454 | 0.62 | 0.77 | 33 | MG |
Interfaces
5 interfaces between chains.
- A–C · 2003 Ų buried · 54 hydrogen bonds · protein-nucleic
- B–D · 1999 Ų buried · 58 hydrogen bonds · protein-nucleic
- A–B · 428 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 254 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 38 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 2ZXU · Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) and… · 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 2ZXU · PDBe 2ZXU · UniProt P16384
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