Research workbench
X-ray crystal analysis of bilirubin oxidase from myrothecium verrucaria at 2.3 ångström resolution using a twin crystal
Analyse X-ray crystal analysis of bilirubin oxidase from myrothecium verrucaria at 2.3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ABG
- Type
- protein
- Length
- 1,026 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bilirubin oxidase
- EC
- 1.3.3.5
- UniProt
- Q12737
- Ligands
- NAG, BMA, CU
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bilirubin oxidase (EC 1.3.3.5) | protein | 508 | 4% helix, 33% strand | Q12737 |
| B | Bilirubin oxidase (EC 1.3.3.5) | protein | 518 | 3% helix, 30% strand | Q12737 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CU · Copper (II) ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.87 | 0.90 | 126 | empty |
| 2 | 187 | 0.69 | 0.87 | 25 | empty |
| 3 | 192 | 0.66 | 0.85 | 30 | empty |
| 4 | 173 | 0.63 | 0.85 | 28 | empty |
| 5 | 89 | 0.63 | 0.90 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1235 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- Q12737 · AlphaFold monomer V2.0 prediction for bilirubin oxidase (Q12737) · a predicted model of the same protein · chain A against A, TM-score 0.93
- 3ABG · X-ray Crystal Analysis of Bilirubin Oxidase from Myrothecium verrucaria at 2.3 angstrom… · the same entry in another collection · chain A against A, TM-score 0.92
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 3ABG · PDBe 3ABG · UniProt Q12737
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