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Structure of the michaelis complex of beta-mannosidase, MAN2A, provides insight into the conformational itinerary of mannoside hydrolysis
Analyse Structure of the michaelis complex of beta-mannosidase, MAN2A, provides insight… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WBK
- Type
- protein
- Length
- 1,677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- EC
- 3.2.1.25
- UniProt
- Q8AAK6
- Ligands
- M2F, BR, CL
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase (EC 3.2.1.25) | protein | 837 | 23% helix, 36% strand | Q8AAK6 |
| B | Beta-mannosidase (EC 3.2.1.25) | protein | 840 | 23% helix, 36% strand | Q8AAK6 |
Ligands and binding sites
- M2F · 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-mannopyranoside · ligand · 2 copies · chains A, B
- BR · Bromide ion · ion · 12 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 38 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.78 | 0.84 | 53 | CL, EDO |
| 2 | 615 | 0.77 | 0.83 | 51 | EDO |
| 3 | 721 | 0.73 | 0.79 | 76 | EDO, BR |
| 4 | 130 | 0.65 | 0.88 | 26 | EDO |
| 5 | 515 | 0.65 | 0.77 | 40 | EDO |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2WBK · Structure of the Michaelis complex of beta-mannosidase, Man2A, provides insight into the… · 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 Q8AAK6
- Elsewhere: RCSB PDB 2WBK · PDBe 2WBK · UniProt Q8AAK6
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