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High resolution structure of bilirubin oxidase from Myrothecium verrucaria - M467Q mutant, anaerobically prepared
Analyse High resolution structure of bilirubin oxidase from Myrothecium verrucaria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IQY
- Type
- protein
- Length
- 1,072 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Myrothecium verrucaria
- Molecule
- Bilirubin oxidase
- EC
- 1.3.3.5
- UniProt
- Q12737
- Ligands
- NAG, MAN, CU, CA
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bilirubin oxidase (EC 1.3.3.5) | protein | 536 | 12% helix, 40% strand | Q12737 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CU · Copper (II) ion · metal · 8 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains B
- GOL · Glycerol · additive · 7 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.74 | 0.77 | 99 | GOL |
| 2 | 111 | 0.49 | 0.81 | 25 | empty |
| 3 | 119 | 0.46 | 0.79 | 23 | empty |
| 4 | 69 | 0.38 | 0.79 | 17 | empty |
| 5 | 61 | 0.29 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 602 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 6IQY · High resolution structure of bilirubin oxidase from myrothecium verrucaria - M467Q… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12737 · AlphaFold monomer V2.0 prediction for bilirubin oxidase (Q12737) · a predicted model of the same protein · chain B 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 Q12737
- Elsewhere: RCSB PDB 6IQY · PDBe 6IQY · UniProt Q12737
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