Research workbench
Crystal structure of lysyl-tRNA synthetase from plasmodium falciparum complexed with a chromone ligand
Analyse Crystal structure of lysyl-tRNA synthetase from plasmodium falciparum complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HCV
- Type
- protein
- Length
- 959 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- Q8IDJ8
- Ligands
- FYE
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 480 | 32% helix, 26% strand | Q8IDJ8 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 479 | 32% helix, 26% strand | Q8IDJ8 |
Ligands and binding sites
- FYE · 6-fluoranyl-~{N}-[(1-oxidanylcyclohexyl)methyl]-4-oxidanylidene-chromene-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.84 | 0.96 | 58 | empty |
| 2 | 930 | 0.78 | 0.80 | 89 | FYE |
| 3 | 906 | 0.77 | 0.80 | 84 | FYE |
| 4 | 214 | 0.61 | 0.82 | 29 | empty |
| 5 | 147 | 0.57 | 0.83 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 4673 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6HCV · Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with a… · 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 Q8IDJ8
- Elsewhere: RCSB PDB 6HCV · PDBe 6HCV · UniProt Q8IDJ8
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