Research workbench
Ternary complex of E. COLI leucyl-tRNA synthetase, TRNA(LEU) and the benzoxaborole AN2679 in the editing conformation
Analyse Ternary complex of E. COLI leucyl-tRNA synthetase, TRNA(LEU) and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ARI
- Type
- protein + RNA
- Length
- 901 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase; TRNA-LEU5 (uaa isoaceptor)
- EC
- 6.1.1.4
- UniProt
- P07813
- Ligands
- MG
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 821 | 40% helix, 21% strand | P07813 |
| B | TRNA-LEU5 (uaa isoaceptor) | rna | 80 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.70 | 0.84 | 41 | empty |
| 2 | 427 | 0.68 | 0.81 | 34 | empty |
| 3 | 389 | 0.68 | 0.81 | 38 | empty |
| 4 | 507 | 0.65 | 0.77 | 51 | empty |
| 5 | 180 | 0.61 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2572 Ų buried · 38 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4ARI · Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and the benzoxaborole AN2679… · the same entry in another collection · chain A against A, TM-score 1.00
- P07813 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (P07813) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P07813
- Elsewhere: RCSB PDB 4ARI · PDBe 4ARI · UniProt P07813
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