MolNFT v1 · #143781 · protein
Structure of gh 38 jack bean alpha-mannosidase in complex with a 36- valent iminosugar cluster inhibitor
6B9P · Alpha-mannosidase from canavalia ensiformis (jack bean): “Structure of gh 38 jack bean alpha-mannosidase in complex with a 36- valent iminosugar cluster inhibitor”. X-ray diffraction, 5 ligands (D0J, MAN, NAG), 20 pockets (best…
- PDB
- 6B9P
- Type
- protein
- Length
- 1,862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-mannosidase from canavalia ensiformis (jack bean)
- EC
- 3.2.1.24
- Ligands
- D0J, MAN, NAG, BMA, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-mannosidase from canavalia ensiformis (jack bean) (EC 3.2.1.24) | protein | 933 | 26% helix, 30% strand | — |
| B | Alpha-mannosidase from canavalia ensiformis (jack bean) (EC 3.2.1.24) | protein | 929 | 26% helix, 29% strand | — |
Ligands and binding sites
- D0J · (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{9-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]nonyl}piperidine-3,4,5-triol · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.84 | 0.85 | 74 | NAG, BMA, MAN |
| 2 | 1174 | 0.84 | 0.85 | 74 | NAG, BMA |
| 3 | 539 | 0.74 | 0.82 | 58 | empty |
| 4 | 55 | 0.71 | 0.98 | 20 | empty |
| 5 | 51 | 0.69 | 0.97 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2362 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6B9P · Structure of GH 38 Jack Bean alpha-mannosidase in complex with a 36-valent iminosugar… · 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 6B9P · PDBe 6B9P
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