Research workbench
Vibrio cholerae family 3 glycoside hydrolase (nagz) bound to N- valeryl-pugnac
Analyse Vibrio cholerae family 3 glycoside hydrolase (nagz) bound to N- valeryl-pugnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GSM
- Type
- protein
- Length
- 324 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
- VPU
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 324 | 42% helix, 13% strand | Q9KU37 |
Ligands and binding sites
- VPU · [[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(pentanoylamino)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 | 273 | 0.58 | 0.77 | 26 | VPU |
| 2 | 180 | 0.56 | 0.80 | 21 | empty |
Compared structures
- 3GSM · Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-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 3GSM · PDBe 3GSM · UniProt Q9KU37
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