MolNFT v1 · #93203 · protein
Crystal structure of salmonella typhimurium family 3 glycoside hydrolase (nagz)
4GVG · Beta-hexosaminidase: “Crystal structure of salmonella typhimurium family 3 glycoside hydrolase (nagz)”. X-ray diffraction, 3 pockets (best druggability 0.66). MolNFT v1 #93203 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4GVG
- Type
- protein
- Length
- 661 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
- Pockets
- 3 · best druggability 0.66
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 | 331 | 48% helix, 12% strand | Q8ZQ06 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 330 | 48% helix, 12% strand | Q8ZQ06 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.66 | 0.82 | 32 | empty |
| 2 | 293 | 0.60 | 0.78 | 29 | empty |
| 3 | 245 | 0.53 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 664 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4GVG · 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 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 4GVG · PDBe 4GVG · UniProt Q8ZQ06
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.