Research workbench
Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis complexed with L-lysine and Cladosporin
Analyse Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NS0
- Type
- protein
- Length
- 1,034 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Chlamydia trachomatis serovar L2b (strain UCH-1/proctitis)
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- B0BAN6
- Ligands
- LYS, KRS, NA, CL
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 517 | 37% helix, 26% strand | B0BAN6 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- KRS · cladosporin · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 34 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.85 | 0.86 | 144 | EDO |
| 2 | 903 | 0.80 | 0.82 | 102 | LYS, KRS, PG4, EDO |
| 3 | 832 | 0.77 | 0.81 | 78 | LYS, KRS, PG4, EDO |
| 4 | 56 | 0.69 | 0.96 | 24 | empty |
| 5 | 156 | 0.67 | 0.88 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 4585 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 6NS0 · Crystal structure of lysyl-tRNA synthetase from chlamydia trachomatis 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 6NS0 · PDBe 6NS0 · UniProt B0BAN6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.