Research workbench
Lysyl-tRNA synthetase (lysu) (E.C.6.1.1.6) complexed with lysine
Analyse Lysyl-tRNA synthetase (lysu) (E.C.6.1.1.6) complexed with lysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LYL
- Type
- protein
- Length
- 1,447 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl-tRNA synthetase (lysu)
- EC
- 6.1.1.6
- UniProt
- P0A8N5
- Ligands
- LYS
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysyl-tRNA synthetase (lysu) (EC 6.1.1.6) | protein | 482 | 38% helix, 27% strand | P0A8N5 |
| B | Lysyl-tRNA synthetase (lysu) (EC 6.1.1.6) | protein | 483 | 38% helix, 27% strand | P0A8N5 |
Ligands and binding sites
- LYS · Lysine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.74 | 0.81 | 60 | LYS |
| 2 | 617 | 0.73 | 0.80 | 60 | LYS |
| 3 | 666 | 0.73 | 0.80 | 62 | LYS |
| 4 | 240 | 0.73 | 0.88 | 39 | empty |
| 5 | 268 | 0.73 | 0.86 | 42 | empty |
Interfaces
1 interface between chains.
- A–C · 4502 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 1LYL · Lysyl-tRNA synthetase (lysu) (E.C.6.1.1.6) complexed with lysine · the same entry in another collection · chain A against A, TM-score 1.00
- P0A8N5 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase, heat inducible (P0A8N5) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P0A8N5
- Elsewhere: RCSB PDB 1LYL · PDBe 1LYL · UniProt P0A8N5
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