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Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum bound to a difluoro cyclohexyl chromone ligand
Analyse Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HCU
- Type
- protein
- Length
- 970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.62
- Source
- Plasmodium falciparum 3D7
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- Q8IDJ8
- Ligands
- FYB, LYS, HIS
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.62 · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 33% helix, 26% strand | Q8IDJ8 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 32% helix, 26% strand | Q8IDJ8 |
Ligands and binding sites
- FYB · ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide · ligand · 2 copies · chains A, B
- LYS · Lysine · ligand · chains A, B
- HIS · Histidine · ligand · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.84 | 0.97 | 51 | TRS |
| 2 | 1051 | 0.78 | 0.80 | 91 | PEG, FYB, TRS |
| 3 | 352 | 0.69 | 0.82 | 37 | empty |
| 4 | 533 | 0.69 | 0.79 | 51 | FYB, TRS |
| 5 | 219 | 0.63 | 0.82 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 4684 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6HCU · Crystal structure of lysyl-tRNA synthetase from plasmodium falciparum bound to a difluoro… · 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 6HCU · PDBe 6HCU · UniProt Q8IDJ8
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