MolNFT v1 · #156338 · protein
Crystal structure of lysyl-tRNA synthetase from plasmodium falciparum complexed with L-lysine and cladosporin derivative (cl-2)
6M0T · Lysine--tRNA ligase: “Crystal structure of lysyl-tRNA synthetase from plasmodium falciparum complexed with L-lysine and cladosporin…”. X-ray diffraction, 2 ligands (LYS, EZ3), 20 pockets (best druggability 0.84). MolNFT v1 #156338…
- PDB
- 6M0T
- Type
- protein
- Length
- 1,952 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
- Q8IDJ8
- Ligands
- LYS, EZ3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 493 | 32% helix, 25% strand | Q8IDJ8 |
| B, D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 487 | 32% helix, 26% strand | Q8IDJ8 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 30% helix, 26% strand | Q8IDJ8 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- EZ3 · (3R)-3-[(R)-[(2R,6S)-6-methyloxan-2-yl]-oxidanyl-methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.84 | 0.96 | 58 | empty |
| 2 | 203 | 0.83 | 0.97 | 44 | empty |
| 3 | 978 | 0.78 | 0.80 | 80 | LYS, EZ3 |
| 4 | 690 | 0.75 | 0.81 | 64 | LYS, EZ3 |
| 5 | 674 | 0.75 | 0.81 | 69 | LYS, EZ3 |
Interfaces
3 interfaces between chains.
- A–B · 4640 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 4598 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6M0T · 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 6M0T · PDBe 6M0T · UniProt Q8IDJ8
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