Research workbench
Ternary complex of E .COLI leucyl-tRNA synthetase, TRNA(LEU) and the benzoxaborole AN3016 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
- 3ZJU
- Type
- protein + RNA
- Length
- 900 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase; TRNALEU5 uaa isoacceptor
- EC
- 6.1.1.4
- UniProt
- P07813
- Ligands
- MG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 820 | 40% helix, 20% strand | P07813 |
| B | TRNALEU5 uaa isoacceptor | rna | 80 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.77 | 0.81 | 84 | empty |
| 2 | 845 | 0.76 | 0.81 | 70 | empty |
| 3 | 306 | 0.68 | 0.83 | 32 | empty |
| 4 | 223 | 0.55 | 0.79 | 20 | empty |
| 5 | 197 | 0.49 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2449 Ų buried · 32 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3ZJU · Ternary complex of E .coli leucyl-tRNA synthetase, tRNA(Leu) and the benzoxaborole AN3016… · 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 3ZJU · PDBe 3ZJU · UniProt P07813
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