MolNFT v1 · #52926 · protein
Structure of the human cytosolic leucyl-tRNA synthetase editing domain
2WFD · Leucyl-tRNA synthetase, cytoplasmic: “Structure of the human cytosolic leucyl-tRNA synthetase editing domain”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #52926 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2WFD
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase, cytoplasmic
- EC
- 6.1.1.4
- UniProt
- Q9P2J5
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Leucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.4) | protein | 252 | 33% helix, 22% strand | Q9P2J5 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.73 | 0.79 | 80 | empty |
| 2 | 256 | 0.67 | 0.83 | 33 | empty |
| 3 | 213 | 0.61 | 0.81 | 42 | empty |
| 4 | 59 | 0.48 | 0.84 | 14 | empty |
| 5 | 108 | 0.39 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1409 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2WFD · Structure of the human cytosolic leucyl-tRNA synthetase editing domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P2J5 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase, cytoplasmic (Q9P2J5) · a predicted model of the same protein · chain A 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 Q9P2J5
- Elsewhere: RCSB PDB 2WFD · PDBe 2WFD · UniProt Q9P2J5
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