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Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 4
Analyse Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KCN
- Type
- protein
- Length
- 1,998 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- W7JP72
- Ligands
- D5F, LYS
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 499 | 35% helix, 25% strand | W7JP72 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 500 | 34% helix, 25% strand | W7JP72 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 497 | 33% helix, 26% strand | W7JP72 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 502 | 34% helix, 25% strand | W7JP72 |
Ligands and binding sites
- D5F · 3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)isochromen-1-one · ligand · 4 copies · chains A, B, C, D
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.82 | 0.96 | 54 | empty |
| 2 | 204 | 0.82 | 0.96 | 58 | GOL |
| 3 | 658 | 0.77 | 0.83 | 63 | D5F, LYS |
| 4 | 700 | 0.77 | 0.82 | 69 | D5F, LYS |
| 5 | 823 | 0.77 | 0.81 | 89 | D5F, LYS |
Interfaces
5 interfaces between chains.
- A–B · 4723 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 4717 Ų buried · 60 hydrogen bonds · protein-protein
- A–D · 329 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KCN · Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin… · 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 W7JP72
- Elsewhere: RCSB PDB 6KCN · PDBe 6KCN · UniProt W7JP72
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