Research workbench
Crystal structure of lysk from thermus thermophilus in complex with lysine
Analyse Crystal structure of lysk from thermus thermophilus in complex with lysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XOY
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [lysw]-lysine hydrolase
- EC
- 3.5.1.-
- UniProt
- Q8VUS5
- Ligands
- LYS, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [lysw]-lysine hydrolase (EC 3.5.1.-) | protein | 341 | 36% helix, 28% strand | Q8VUS5 |
| B | [lysw]-lysine hydrolase (EC 3.5.1.-) | protein | 349 | 34% helix, 29% strand | Q8VUS5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.72 | 0.83 | 62 | LYS |
| 2 | 581 | 0.65 | 0.76 | 57 | empty |
| 3 | 84 | 0.44 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1292 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5XOY · Crystal structure of LysK from Thermus thermophilus in complex with Lysine · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VUS5 · AlphaFold monomer V2.0 prediction for [lysw]-lysine hydrolase (Q8VUS5) · a predicted model of the same protein · chain B 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 Q8VUS5
- Elsewhere: RCSB PDB 5XOY · PDBe 5XOY · UniProt Q8VUS5
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