MolNFT v1 · #158748 · protein
Crystal structure of lysyl-tRNA synthetase from chlamydia trachomatis with complexed with L-lysine and a difluoro cyclohexyl chromone ligand
6O3F · Lysine--tRNA ligase: “Crystal structure of lysyl-tRNA synthetase from chlamydia trachomatis with complexed with L-lysine and a…”. X-ray diffraction, 3 ligands (FYB, LYS, SO4), 13 pockets (best druggability 0.90). MolNFT v1 #158748…
- PDB
- 6O3F
- Type
- protein
- Length
- 1,034 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
- B0BAN6
- Ligands
- FYB, LYS, SO4
- Pockets
- 13 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 517 | 36% helix, 26% strand | B0BAN6 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 517 | 36% helix, 25% strand | B0BAN6 |
Ligands and binding sites
- FYB · ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide · ligand · 2 copies · chains A, B
- LYS · Lysine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.90 | 0.92 | 176 | EDO, PEG, SO4, FYB, PG4, LYS |
| 2 | 162 | 0.70 | 0.89 | 31 | FYB, LYS |
| 3 | 82 | 0.52 | 0.84 | 17 | empty |
| 4 | 70 | 0.48 | 0.83 | 16 | PEG |
| 5 | 144 | 0.46 | 0.77 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 4587 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 6O3F · Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- B0BAN6 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (B0BAN6) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 B0BAN6
- Elsewhere: RCSB PDB 6O3F · PDBe 6O3F · UniProt B0BAN6
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