Research workbench
Crystal structure of beta-D-mannosidase from dictyoglomus thermophilum.
Analyse Crystal structure of beta-D-mannosidase from dictyoglomus thermophilum. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N6U
- Type
- protein
- Length
- 3,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- EC
- 3.2.1.25
- UniProt
- B5YAN4
- Ligands
- BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-mannosidase (EC 3.2.1.25) | protein | 811 | 22% helix, 34% strand | B5YAN4 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 4 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 | 727 | 0.84 | 0.87 | 86 | empty |
| 2 | 635 | 0.83 | 0.87 | 77 | empty |
| 3 | 418 | 0.77 | 0.86 | 50 | empty |
| 4 | 406 | 0.77 | 0.86 | 50 | empty |
| 5 | 597 | 0.74 | 0.81 | 69 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1703 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1650 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1218 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1188 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5N6U · Crystal structure of Beta-D-Mannosidase from Dictyoglomus thermophilum. · 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 B5YAN4
- Elsewhere: RCSB PDB 5N6U · PDBe 5N6U · UniProt B5YAN4
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