MolNFT v1 · #146314 · protein
Mouse beta-mannosidase bound to beta-D-mannose (manba)
6DDU: “Mouse beta-mannosidase bound to beta-D-mannose (manba)”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 10 pockets (best druggability 0.66). MolNFT v1 #146314 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DDU
- Type
- protein
- Length
- 862 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- EC
- 3.2.1.25
- UniProt
- Q8K2I4
- Ligands
- NAG, FUC, BMA, CA
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase (EC 3.2.1.25) | protein | 862 | 24% helix, 33% strand | Q8K2I4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.66 | 0.80 | 35 | BMA, EDO |
| 2 | 657 | 0.66 | 0.75 | 64 | empty |
| 3 | 176 | 0.64 | 0.84 | 25 | empty |
| 4 | 129 | 0.58 | 0.84 | 21 | empty |
| 5 | 212 | 0.57 | 0.80 | 35 | empty |
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
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 Q8K2I4
- Elsewhere: RCSB PDB 6DDU · PDBe 6DDU · UniProt Q8K2I4
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