Research workbench
Structure of fungal beta-mannosidase (GH2) from trichoderma harzianum
Analyse Structure of fungal beta-mannosidase (GH2) from trichoderma harzianum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UOJ
- Type
- protein
- Length
- 1,834 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase GH2
- Ligands
- MAN, NAG, BMA, CD, NA, CA, CL
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-mannosidase GH2 | protein | 917 | 25% helix, 31% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 35 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- CD · Cadmium ion · metal · 28 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · chains B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.83 | 0.84 | 136 | CD |
| 2 | 167 | 0.81 | 0.96 | 19 | empty |
| 3 | 173 | 0.80 | 0.95 | 20 | empty |
| 4 | 100 | 0.64 | 0.90 | 29 | empty |
| 5 | 201 | 0.61 | 0.82 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4UOJ · Structure of Fungal beta-mannosidase (GH2) from Trichoderma harzianum · 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
- Elsewhere: RCSB PDB 4UOJ · PDBe 4UOJ
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