MolNFT v1 · #154412 · protein
Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 2
6KAB · Lysine--tRNA ligase: “Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 2”. X-ray diffraction, 2 ligands (D4U, LYS), 20 pockets (best druggability 0.81). MolNFT v1 #154412 on GenesisL1…
- PDB
- 6KAB
- Type
- protein
- Length
- 2,008 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
- D4U, LYS
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 506 | 33% helix, 25% strand | W7JP72 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 503 | 34% helix, 25% strand | W7JP72 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 498 | 33% helix, 26% strand | W7JP72 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 501 | 33% helix, 26% strand | W7JP72 |
Ligands and binding sites
- D4U · (3~{S})-3-(cyclohexylmethyl)-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one · ligand · 4 copies · chains A, B, C, D
- LYS · Lysine · ligand · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.81 | 0.95 | 47 | empty |
| 2 | 162 | 0.79 | 0.96 | 35 | empty |
| 3 | 959 | 0.79 | 0.81 | 98 | D4U, LYS |
| 4 | 708 | 0.78 | 0.83 | 74 | D4U, LYS |
| 5 | 810 | 0.78 | 0.82 | 80 | D4U, LYS |
Interfaces
4 interfaces between chains.
- A–B · 4746 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 4741 Ų buried · 59 hydrogen bonds · protein-protein
- A–D · 232 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 90 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6KAB · 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 6KAB · PDBe 6KAB · UniProt W7JP72
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