Research workbench
Bilirubin oxidase from myrothecium verrucaria, mutant W396A in complex with ferricyanide
Analyse Bilirubin oxidase from myrothecium verrucaria, mutant W396A in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I3K
- Type
- protein
- Length
- 1,068 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
- FC6, NAG, BMA, CU, NA, K
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bilirubin oxidase (EC 1.3.3.5) | protein | 534 | 11% helix, 39% strand | Q12737 |
Ligands and binding sites
- FC6 · Hexacyanoferrate(3-) · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- CU · Copper (II) ion · metal · 8 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- SIN · Succinic acid · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.58 | 0.75 | 52 | GOL |
| 2 | 348 | 0.55 | 0.74 | 45 | empty |
| 3 | 167 | 0.49 | 0.77 | 24 | empty |
| 4 | 144 | 0.45 | 0.76 | 19 | empty |
| 5 | 62 | 0.42 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 435 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 6I3K · Bilirubin oxidase from Myrothecium verrucaria, mutant W396A in complex with ferricyanide · 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 6I3K · PDBe 6I3K · UniProt Q12737
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