Research workbench
Crystal structure of native beta-N-acetylhexosaminidase isolated from aspergillus oryzae
Analyse Crystal structure of native beta-N-acetylhexosaminidase isolated from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OAR
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q8J2T0
- Ligands
- NGT, TBR, NAG, MAN, BMA, CL
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 72 | 22% helix, 19% strand | Q8J2T0 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 497 | 33% helix, 19% strand | Q8J2T0 |
| C | Beta-hexosaminidase (EC 3.2.1.52) | protein | 73 | 22% helix, 21% strand | Q8J2T0 |
| D | Beta-hexosaminidase (EC 3.2.1.52) | protein | 498 | 32% helix, 18% strand | Q8J2T0 |
Ligands and binding sites
- NGT · 3ar,5r,6s,7r,7ar-5-hydroxymethyl-2-methyl-5,6,7,7A-tetrahydro-3AH-pyrano[3,2-d]thiazole-6,7-diol · ligand · 2 copies · chains B, D
- TBR · Hexatantalum dodecabromide · ligand · chains D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, C, A, D
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, D, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CL · Chloride ion · ion · 11 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.69 | 0.84 | 34 | NGT, CL |
| 2 | 253 | 0.68 | 0.84 | 36 | NGT, CL |
| 3 | 88 | 0.41 | 0.78 | 20 | empty |
| 4 | 88 | 0.39 | 0.77 | 25 | empty |
| 5 | 91 | 0.36 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–D · 3815 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 3159 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3151 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 353 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 338 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 glycan, 6 disulfide (disulfide, O-glycosylation, N-glycosylation).
Compared structures
- 5OAR · Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae · the same entry in another collection · chain D against D, TM-score 1.00
- Q8J2T0 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (Q8J2T0) · a predicted model of the same protein · chain B 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 Q8J2T0
- Elsewhere: RCSB PDB 5OAR · PDBe 5OAR · UniProt Q8J2T0
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