MolNFT v1 · #119748 · protein
Crystal structure of nagz from pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin
5G5K · Beta-hexosaminidase: “Crystal structure of nagz from pseudomonas aeruginosa in complex with the inhibitor…”. X-ray diffraction, 1 ligand (NOK), 4 pockets (best druggability 0.73). MolNFT v1 #119748 on GenesisL1: 3D structure…
- PDB
- 5G5K
- Type
- protein
- Length
- 665 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 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 333 | 38% helix, 13% strand | Q9HZK0 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 332 | 38% helix, 12% strand | Q9HZK0 |
Ligands and binding sites
- NOK · 2-acetamido-1,2-dideoxynojirmycin · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.73 | 0.78 | 73 | NOK |
| 2 | 175 | 0.61 | 0.83 | 24 | NOK |
| 3 | 63 | 0.29 | 0.74 | 18 | empty |
| 4 | 65 | 0.28 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 545 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5G5K · Crystal structure of NagZ from Pseudomonas aeruginosa in complex with the inhibitor… · 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 B against A, TM-score 0.98
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 5G5K · PDBe 5G5K · UniProt Q9HZK0
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