MolNFT v1 · #151972 · protein
Bilirubin oxidase from myrothecium verrucaria in complex with ferricyanide
6I3J: “Bilirubin oxidase from myrothecium verrucaria in complex with ferricyanide”. X-ray diffraction, 7 ligands (FC6, NAG, BMA), 6 pockets (best druggability 0.84). MolNFT v1 #151972 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6I3J
- Type
- protein
- Length
- 1,067 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, MAN, CU, NA, CL
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bilirubin oxidase (EC 1.3.3.5) | protein | 534 | 12% helix, 39% strand | Q12737 |
| B | Bilirubin oxidase (EC 1.3.3.5) | protein | 533 | 12% helix, 40% strand | Q12737 |
Ligands and binding sites
- FC6 · Hexacyanoferrate(3-) · ligand · 9 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
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- CU · Copper (II) ion · metal · 8 copies · chains A, B
- NA · Sodium ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · chains A
- SIN · Succinic acid · additive · 5 copies · chains A, B
- PGR · R-1,2-propanediol · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.84 | 0.85 | 86 | NA |
| 2 | 98 | 0.61 | 0.87 | 30 | SIN |
| 3 | 78 | 0.44 | 0.81 | 23 | empty |
| 4 | 60 | 0.41 | 0.81 | 20 | empty |
| 5 | 69 | 0.38 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 878 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 6I3J · Bilirubin oxidase from Myrothecium verrucaria 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 6I3J · PDBe 6I3J · UniProt Q12737
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