Research workbench
Crystal structure of nagz H174A mutant from pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin
Analyse Crystal structure of nagz H174A mutant from pseudomonas aeruginosa in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LY7
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q9HZK0
- Ligands
- NOK
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 333 | 44% helix, 14% strand | Q9HZK0 |
Ligands and binding sites
- NOK · 2-acetamido-1,2-dideoxynojirmycin · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.71 | 0.78 | 53 | PEG |
| 2 | 193 | 0.59 | 0.81 | 25 | NOK |
| 3 | 183 | 0.58 | 0.81 | 24 | NOK |
| 4 | 142 | 0.45 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 529 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5LY7 · Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HZK0 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (Q9HZK0) · a predicted model of the same protein · chain A 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 Q9HZK0
- Elsewhere: RCSB PDB 5LY7 · PDBe 5LY7 · UniProt Q9HZK0
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