Research workbench
Crystal structure of the P.KNOWLESI cytosolic leucyl-tRNA synthetase editing domain
Analyse Crystal structure of the P.KNOWLESI cytosolic leucyl-tRNA synthetase editing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FOF
- Type
- protein
- Length
- 1,193 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase
- EC
- 6.1.1.4
- UniProt
- B3L7I1
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 302 | 36% helix, 23% strand | B3L7I1 |
| B | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 290 | 34% helix, 22% strand | B3L7I1 |
| C | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 299 | 33% helix, 22% strand | B3L7I1 |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.73 | 0.92 | 34 | empty |
| 2 | 111 | 0.70 | 0.92 | 31 | empty |
| 3 | 117 | 0.69 | 0.91 | 29 | empty |
| 4 | 107 | 0.69 | 0.92 | 30 | empty |
| 5 | 832 | 0.68 | 0.75 | 85 | empty |
Interfaces
5 interfaces between chains.
- B–D · 510 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 259 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 198 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 196 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FOF · Crystal structure of the P.knowlesi cytosolic leucyl-tRNA synthetase editing domain · the same entry in another collection · chain A against A, TM-score 1.00
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 B3L7I1
- Elsewhere: RCSB PDB 5FOF · PDBe 5FOF · UniProt B3L7I1
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