MolNFT v1 · #154450 · protein
Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 3
6KBF · Lysine--tRNA ligase: “Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 3”. X-ray diffraction, 2 ligands (LYS, D4X), 15 pockets (best druggability 0.83). MolNFT v1 #154450 on GenesisL1…
- PDB
- 6KBF
- Type
- protein
- Length
- 1,007 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
- W7JP72
- Ligands
- LYS, D4X
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 504 | 34% helix, 25% strand | W7JP72 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 503 | 34% helix, 25% strand | W7JP72 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- D4X · (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6, 8-bis(oxidanyl)-3,4-dihydro-2~{H}-isoquinolin-1-one · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.83 | 0.96 | 60 | GOL |
| 2 | 718 | 0.79 | 0.84 | 73 | LYS, D4X |
| 3 | 912 | 0.78 | 0.81 | 88 | LYS, D4X |
| 4 | 288 | 0.75 | 0.87 | 32 | empty |
| 5 | 274 | 0.74 | 0.87 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 4535 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 6KBF · Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin… · 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 W7JP72
- Elsewhere: RCSB PDB 6KBF · PDBe 6KBF · UniProt W7JP72
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.