Research workbench
Crystal structure of salmonella typhimurium family 3 glycoside hydrolase (nagz) covalently bound to 5-fluoro-glcnac.
Analyse Crystal structure of salmonella typhimurium family 3 glycoside hydrolase (nagz)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GVH
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q8ZQ06
- Ligands
- 0XY
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 341 | 48% helix, 12% strand | Q8ZQ06 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 328 | 48% helix, 12% strand | Q8ZQ06 |
Ligands and binding sites
- 0XY · 5-fluoro-N-acetyl-alpha-D-glucosamine · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
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 | 76 | 0.68 | 0.94 | 19 | empty |
| 2 | 114 | 0.63 | 0.88 | 25 | empty |
| 3 | 256 | 0.56 | 0.77 | 36 | 0XY |
| 4 | 139 | 0.44 | 0.76 | 23 | 0XY |
| 5 | 70 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 740 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4GVH · Crystal structure of Salmonella typhimurium family 3 glycoside hydrolase (NagZ)… · 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 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 Q8ZQ06
- Elsewhere: RCSB PDB 4GVH · PDBe 4GVH · UniProt Q8ZQ06
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