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Crystallographic structure of oligosaccharide dehydrogenase from pycnoporus cinnabarinus, ligand-free form
Analyse Crystallographic structure of oligosaccharide dehydrogenase from pycnoporus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XUT
- Type
- protein
- Length
- 589 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligosaccharide dehydrogenase
- UniProt
- A0A060SC37
- Ligands
- FAD, NAG, BMA, SO4
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligosaccharide dehydrogenase | protein | 589 | 35% helix, 21% strand | A0A060SC37 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- SO4 · Sulfate ion · ion · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.82 | 0.86 | 83 | FAD |
| 2 | 141 | 0.40 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 6XUT · Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus… · 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 A0A060SC37
- Elsewhere: RCSB PDB 6XUT · PDBe 6XUT · UniProt A0A060SC37
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