Research workbench
Crystal structure of lysyl-tRNA synthetase from plasmodium falciparum complexed with L-lysine and clado-B
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
- 6L4Q
- Type
- protein
- Length
- 972 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
- E5R, LYS
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 31% helix, 25% strand | Q8IDJ8 |
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 487 | 27% helix, 25% strand | Q8IDJ8 |
Ligands and binding sites
- E5R · (3R)-3-[[(3R)-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one · ligand · 2 copies · chains B, A
- LYS · Lysine · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.78 | 0.87 | 72 | empty |
| 2 | 628 | 0.75 | 0.82 | 68 | E5R, LYS |
| 3 | 676 | 0.75 | 0.81 | 60 | E5R, LYS |
| 4 | 237 | 0.71 | 0.86 | 27 | empty |
| 5 | 276 | 0.70 | 0.84 | 37 | empty |
Interfaces
1 interface between chains.
- B–A · 4620 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6L4Q · Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with… · the same entry in another collection · chain B against B, 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 6L4Q · PDBe 6L4Q · UniProt Q8IDJ8
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