MolNFT v1 · #65272 · protein
Vibrio cholerea family 3 glycoside hydrolase (NAGZ)IN complex with N- butyryl-pugnac
3GS6 · Beta-hexosaminidase: “Vibrio cholerea family 3 glycoside hydrolase (NAGZ)IN complex with N- butyryl-pugnac”. X-ray diffraction, 1 ligand (NP6), 2 pockets (best druggability 0.58). MolNFT v1 #65272 on GenesisL1: 3D structure, binding…
- PDB
- 3GS6
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q9KU37
- Ligands
- NP6
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 322 | 44% helix, 13% strand | Q9KU37 |
Ligands and binding sites
- NP6 · [[(3R,4R,5S,6R)-3-(butanoylamino)-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-ylidene]amino] N-phenylcarbamate · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.58 | 0.84 | 19 | empty |
| 2 | 277 | 0.55 | 0.76 | 25 | NP6 |
Compared structures
- 3GS6 · Vibrio Cholerea family 3 glycoside hydrolase (NagZ)in complex with N-butyryl-PUGNAc · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KU37 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (Q9KU37) · a predicted model of the same protein · chain A 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 Q9KU37
- Elsewhere: RCSB PDB 3GS6 · PDBe 3GS6 · UniProt Q9KU37
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