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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
- 5FJI
- Type
- protein
- Length
- 1,680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- P42212
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucosidase (EC 3.2.1.21) | protein | 840 | 27% helix, 19% strand | P42212 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 45 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 14 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 39 copies · chains A, B
- IMD · Imidazole · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.72 | 0.97 | 27 | empty |
| 2 | 231 | 0.61 | 0.81 | 34 | EDO |
| 3 | 240 | 0.61 | 0.81 | 33 | EDO |
| 4 | 185 | 0.61 | 0.83 | 32 | EDO |
| 5 | 194 | 0.60 | 0.82 | 35 | EDO |
Interfaces
1 interface between chains.
- A–B · 1444 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FJI · Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. Family GH3… · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.12
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 P42212
- Elsewhere: RCSB PDB 5FJI · PDBe 5FJI · UniProt P42212
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