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Three-dimensional structures of two heavily N-glycosylated aspergillus sp. family GH3 beta-D-glucosidases
Analyse Three-dimensional structures of two heavily N-glycosylated aspergillus sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FJJ
- Type
- protein
- Length
- 3,354 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- Q2UUD6
- Ligands
- NAG, MAN, BMA, MG, CL, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-glucosidase (EC 3.2.1.21) | protein | 839 | 27% helix, 19% strand | Q2UUD6 |
| B, D | Beta-glucosidase (EC 3.2.1.21) | protein | 838 | 27% helix, 19% strand | Q2UUD6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 66 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 22 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.82 | 0.83 | 99 | empty |
| 2 | 1125 | 0.82 | 0.83 | 95 | empty |
| 3 | 71 | 0.73 | 0.98 | 26 | empty |
| 4 | 470 | 0.69 | 0.80 | 71 | PEG, CL |
| 5 | 122 | 0.69 | 0.90 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1759 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1745 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 782 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FJJ · Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. Family GH3… · the same entry in another collection · chain D against D, TM-score 1.00
- Q2UUD6 · AlphaFold monomer V2.0 prediction for probable beta-glucosidase a (Q2UUD6) · a predicted model of the same protein · chain C 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 Q2UUD6
- Elsewhere: RCSB PDB 5FJJ · PDBe 5FJJ · UniProt Q2UUD6
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