Research workbench
Expansion of the glycosynthase repertoire to produce defined manno- oligosaccharides
Analyse Expansion of the glycosynthase repertoire to produce defined manno… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ODZ
- Type
- protein
- Length
- 758 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan endo-1,4-beta-mannosidase
- EC
- 3.2.1.78
- UniProt
- P49424
- Ligands
- MAN, BMA, ZN, NA
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannan endo-1,4-beta-mannosidase (EC 3.2.1.78) | protein | 379 | 35% helix, 15% strand | P49424 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.69 | 0.95 | 21 | empty |
| 2 | 63 | 0.69 | 0.95 | 19 | empty |
| 3 | 293 | 0.58 | 0.77 | 41 | MAN, BMA |
| 4 | 269 | 0.55 | 0.76 | 26 | MAN, BMA |
| 5 | 129 | 0.37 | 0.73 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 321 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1ODZ · Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides · the same entry in another collection · chain A against A, TM-score 1.00
- P49424 · AlphaFold monomer V2.0 prediction for mannan endo-1,4-beta- mannosidase (P49424) · a predicted model of the same protein · 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 P49424
- Elsewhere: RCSB PDB 1ODZ · PDBe 1ODZ · UniProt P49424
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