MolNFT v1 · #26764 · protein + RNA
The crystal structure of leucyl-tRNA synthetase and TRNA(LEUCINE) complex
1WZ2: “The crystal structure of leucyl-tRNA synthetase and TRNA(LEUCINE) complex”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #26764 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1WZ2
- Type
- protein + RNA
- Length
- 2,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA; Leucyl-tRNA synthetase
- EC
- 6.1.1.4
- UniProt
- O58698
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | TRNA | rna | 88 | — | — |
| A, B | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 948 | 41% helix, 13% strand | O58698 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.79 | 0.82 | 95 | empty |
| 2 | 1137 | 0.78 | 0.80 | 73 | empty |
| 3 | 802 | 0.77 | 0.81 | 79 | empty |
| 4 | 784 | 0.74 | 0.79 | 66 | empty |
| 5 | 348 | 0.73 | 0.84 | 33 | empty |
Interfaces
2 interfaces between chains.
- C–A · 2145 Ų buried · 48 hydrogen bonds · protein-nucleic
- D–B · 1721 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 1WZ2 · The crystal structure of Leucyl-tRNA synthetase and tRNA(leucine) complex · the same entry in another collection · chain C against C, TM-score 1.00
- O58698 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (O58698) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 O58698
- Elsewhere: RCSB PDB 1WZ2 · PDBe 1WZ2 · UniProt O58698
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