Research workbench
The crystal structure of beta-N-acetylhexosaminidase from bacteroides fragilis nctc 9343
Analyse The crystal structure of beta-N-acetylhexosaminidase from bacteroides fragilis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PYS
- Type
- protein
- Length
- 975 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylhexosaminidase
- UniProt
- Q5LAT3
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase | protein | 492 | 37% helix, 19% strand | Q5LAT3 |
| B | Beta-N-acetylhexosaminidase | protein | 483 | 37% helix, 20% strand | Q5LAT3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 10 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.55 | 0.79 | 30 | empty |
| 2 | 229 | 0.50 | 0.75 | 22 | empty |
| 3 | 135 | 0.48 | 0.78 | 19 | GOL, FMT |
| 4 | 119 | 0.46 | 0.78 | 21 | GOL, FMT |
| 5 | 72 | 0.44 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 779 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4PYS · The crystal structure of beta-N-acetylhexosaminidase from Bacteroides fragilis NCTC 9343 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5LAT3
- Elsewhere: RCSB PDB 4PYS · PDBe 4PYS · UniProt Q5LAT3
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