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Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-C
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
- 6L3Y
- Type
- protein
- Length
- 966 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Plasmodium falciparum 3D7
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- Q8IDJ8
- Ligands
- LYS, E5C, PO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · resolution 3.1 · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 484 | 30% helix, 26% strand | Q8IDJ8 |
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 482 | 30% helix, 26% strand | Q8IDJ8 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains B, A
- E5C · (3R)-3-[[(3S)-3-ethylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one · ligand · 2 copies · chains B, A
- PO4 · Phosphate ion · ion · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.81 | 0.97 | 40 | empty |
| 2 | 720 | 0.76 | 0.81 | 68 | LYS, E5C, PO4 |
| 3 | 702 | 0.75 | 0.81 | 58 | LYS, E5C, PO4 |
| 4 | 251 | 0.74 | 0.88 | 34 | empty |
| 5 | 275 | 0.72 | 0.86 | 37 | empty |
Interfaces
1 interface between chains.
- B–A · 4673 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6L3Y · Crystal structure of lysyl-tRNA synthetase from plasmodium falciparum complexed with… · 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 6L3Y · PDBe 6L3Y · UniProt Q8IDJ8
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