Research workbench
Insights into editing from an ile-tRNA synthetase structure with TRNA(ILE) and mupirocin
Analyse Insights into editing from an ile-tRNA synthetase structure with TRNA(ILE) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FFY
- Type
- protein + RNA
- Length
- 992 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoleucyl-tRNA; Isoleucyl-tRNA synthetase
- EC
- 6.1.1.5
- UniProt
- P41972
- Ligands
- MRC, MG, ZN, K
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Isoleucyl-tRNA | rna | 75 | — | — |
| A | Isoleucyl-tRNA synthetase (EC 6.1.1.5) | protein | 917 | 42% helix, 14% strand | P41972 |
Ligands and binding sites
- MRC · Mupirocin · ligand · chains A
- MG · Magnesium ion · metal · 10 copies · chains T, A
- ZN · Zinc ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.83 | 0.96 | 32 | K |
| 2 | 134 | 0.77 | 0.95 | 27 | empty |
| 3 | 715 | 0.73 | 0.79 | 58 | empty |
| 4 | 487 | 0.70 | 0.80 | 35 | empty |
| 5 | 803 | 0.70 | 0.77 | 56 | MG |
Interfaces
1 interface between chains.
- T–A · 2576 Ų buried · 68 hydrogen bonds · protein-nucleic
Compared structures
- 1FFY · Insights into editing from an ile-tRNA synthetase structure with TRNA(ILE) and mupirocin · the same entry in another collection · chain T against T, TM-score 1.00
- P41972 · AlphaFold monomer V2.0 prediction for isoleucine--tRNA ligase (P41972) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P41972
- Elsewhere: RCSB PDB 1FFY · PDBe 1FFY · UniProt P41972
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