MolNFT v1 · #168289 · protein
Crystal structure of lysyl-tRNA synthetase from stenotrophomonas maltophilia with bound L-lysine
6WBD · Lysine--tRNA ligase: “Crystal structure of lysyl-tRNA synthetase from stenotrophomonas maltophilia with bound L-lysine”. X-ray diffraction, 2 ligands (LYS, CL), 10 pockets (best druggability 0.85). MolNFT v1 #168289 on GenesisL1: 3D…
- PDB
- 6WBD
- Type
- protein
- Length
- 964 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
- B2FQ84
- Ligands
- LYS, CL
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 479 | 37% helix, 27% strand | B2FQ84 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 38% helix, 26% strand | B2FQ84 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 50 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.85 | 0.89 | 122 | EDO |
| 2 | 791 | 0.75 | 0.80 | 73 | LYS, EDO |
| 3 | 752 | 0.73 | 0.79 | 71 | LYS, EDO |
| 4 | 179 | 0.49 | 0.77 | 26 | EDO |
| 5 | 134 | 0.46 | 0.77 | 23 | EDO |
Interfaces
1 interface between chains.
- A–B · 4880 Ų buried · 103 hydrogen bonds · protein-protein
Compared structures
- 6WBD · Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas maltophilia with bound… · 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 B2FQ84
- Elsewhere: RCSB PDB 6WBD · PDBe 6WBD · UniProt B2FQ84
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