MolNFT v1 · #152545 · protein
Crystal structure of human lysyl-tRNA synthetase L350H mutant
6ILH · Lysine-tRNA ligase: “Crystal structure of human lysyl-tRNA synthetase L350H mutant”. X-ray diffraction, 1 ligand (KAA), 11 pockets (best druggability 0.84). MolNFT v1 #152545 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6ILH
- Type
- protein
- Length
- 1,006 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
- Q15046
- Ligands
- KAA
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-tRNA ligase (EC 6.1.1.6) | protein | 502 | 36% helix, 25% strand | Q15046 |
| B | Lysine-tRNA ligase (EC 6.1.1.6) | protein | 504 | 36% helix, 25% strand | Q15046 |
Ligands and binding sites
- KAA · 5'-O-[(L-lysylamino)sulfonyl]adenosine · ligand · 2 copies · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.84 | 0.97 | 57 | empty |
| 2 | 883 | 0.79 | 0.82 | 97 | KAA |
| 3 | 865 | 0.79 | 0.82 | 85 | KAA |
| 4 | 289 | 0.72 | 0.85 | 36 | empty |
| 5 | 303 | 0.71 | 0.85 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 4308 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
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 Q15046
- Elsewhere: RCSB PDB 6ILH · PDBe 6ILH · UniProt Q15046
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