Research workbench
Structural and functional studies of glycoside hydrolase family 3 beta-glucosidase CEL3A from the moderately thermophilic fungus rasamsonia emersonii
Analyse Structural and functional studies of glycoside hydrolase family 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JU6
- Type
- protein
- Length
- 3,340 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- Q8TGI8
- Ligands
- MAN, NAG, BMA, BGC, GLC
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-glucosidase (EC 3.2.1.21) | protein | 835 | 27% helix, 19% strand | Q8TGI8 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 83 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 26 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies
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 | 655 | 0.81 | 0.86 | 80 | NAG |
| 2 | 551 | 0.79 | 0.85 | 65 | empty |
| 3 | 96 | 0.78 | 0.99 | 28 | empty |
| 4 | 103 | 0.77 | 0.97 | 28 | empty |
| 5 | 95 | 0.76 | 0.97 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1471 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1440 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 964 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 877 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 345 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 15 disulfide (N-glycosylation, disulfide).
Compared structures
- 5JU6 · Structural and Functional Studies of Glycoside Hydrolase Family 3 beta-Glucosidase Cel3A… · 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 Q8TGI8
- Elsewhere: RCSB PDB 5JU6 · PDBe 5JU6 · UniProt Q8TGI8
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