MolNFT v1 · #26279 · protein
Crystal structure of leucyl-tRNA synthetase from the archaeon pyrococcus horikoshii reveals a novel editing domain orientation
1WKB: “Crystal structure of leucyl-tRNA synthetase from the archaeon pyrococcus horikoshii reveals a novel editing…”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.70). MolNFT v1 #26279 on GenesisL1: 3D structure…
- PDB
- 1WKB
- Type
- protein
- Length
- 791 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase
- EC
- 6.1.1.4
- UniProt
- O58698
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 791 | 46% helix, 18% strand | O58698 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.70 | 0.78 | 78 | SO4 |
| 2 | 356 | 0.68 | 0.82 | 28 | SO4 |
| 3 | 337 | 0.61 | 0.78 | 41 | empty |
| 4 | 90 | 0.51 | 0.83 | 21 | empty |
| 5 | 103 | 0.38 | 0.75 | 20 | empty |
Compared structures
- 1WKB · Crystal Structure of Leucyl-tRNA Synthetase from the Archaeon Pyrococcus horikoshii… · the same entry in another collection · chain A against A, 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 0.99
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 O58698
- Elsewhere: RCSB PDB 1WKB · PDBe 1WKB · UniProt O58698
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