Research workbench
Structure of gh 38 jack bean alpha-mannosidase
Analyse Structure of gh 38 jack bean alpha-mannosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B9O
- Type
- protein
- Length
- 1,872 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
- MAN, NAG, BMA, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-mannosidase from canavalia ensiformis (jack bean) (EC 3.2.1.24) | protein | 935 | 26% helix, 30% strand | — |
| B | Alpha-mannosidase from canavalia ensiformis (jack bean) (EC 3.2.1.24) | protein | 937 | 26% helix, 29% strand | — |
Ligands and binding sites
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.85 | 0.86 | 96 | NAG, BMA |
| 2 | 686 | 0.85 | 0.89 | 49 | empty |
| 3 | 598 | 0.75 | 0.82 | 58 | empty |
| 4 | 476 | 0.69 | 0.79 | 40 | NAG, BMA |
| 5 | 112 | 0.65 | 0.89 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2371 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6B9O · Structure of GH 38 Jack Bean alpha-mannosidase · 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 6B9O · PDBe 6B9O
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