Research workbench
Co-crystal structure of Chaetomium glucosidase with compound 4
Analyse Co-crystal structure of Chaetomium glucosidase with compound 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8E3J
- Type
- protein
- Length
- 1,532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.71
- Source
- Thermochaetoides thermophila DSM 1495
- Molecule
- Chaetomium alpha glucosidase
- UniProt
- G0SFD1
- Ligands
- UGO, NAG, SO4
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.71 · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaetomium alpha glucosidase | protein | 765 | 38% helix, 23% strand | G0SFD1 |
| B | Chaetomium alpha glucosidase | protein | 767 | 38% helix, 23% strand | G0SFD1 |
Ligands and binding sites
- UGO · (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{6-[2-nitro-4-(pyrimidin-2-yl)anilino]hexyl}piperidine-3,4,5-triol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.75 | 0.84 | 58 | SO4 |
| 2 | 415 | 0.74 | 0.84 | 63 | SO4 |
| 3 | 870 | 0.74 | 0.78 | 75 | UGO |
| 4 | 383 | 0.67 | 0.80 | 44 | UGO |
| 5 | 241 | 0.60 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1310 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
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 G0SFD1
- Elsewhere: RCSB PDB 8E3J · PDBe 8E3J · UniProt G0SFD1
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