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Crystal structure of mutant (D248N) Salmonella typhimurium family 3 glycoside hydrolase (NagZ) in complex with GlcNAc-1,6-anhMurNAc
Analyse Crystal structure of mutant (D248N) Salmonella typhimurium family 3 glycoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GVI
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.55
- Source
- Salmonella enterica subsp. enterica serovar Typhimurium
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q8ZQ06
- Ligands
- AH0, NAG
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.55 · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 333 | 48% helix, 13% strand | Q8ZQ06 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 331 | 48% helix, 13% strand | Q8ZQ06 |
Ligands and binding sites
- AH0 · 2-(2-acetylamino-4-hydroxy-6,8-dioxa-bicyclo[3.2.1]oct-3-yloxy)-propionic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.66 | 0.81 | 30 | empty |
| 2 | 383 | 0.64 | 0.78 | 36 | NAG, AH0 |
| 3 | 307 | 0.59 | 0.77 | 25 | AH0, NAG |
| 4 | 73 | 0.30 | 0.73 | 23 | empty |
| 5 | 52 | 0.23 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4GVI · Crystal structure of mutant (D248N) salmonella typhimurium family 3 glycoside hydrolase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZQ06 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (Q8ZQ06) · 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 Q8ZQ06
- Elsewhere: RCSB PDB 4GVI · PDBe 4GVI · UniProt Q8ZQ06
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