› 6i3j

X-ray diffraction
2.59Å resolution

Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide

Released:
DOI: 10.2210/pdb6i3j/pdb
PDB entry 6i3j coloured by chain, front view.
PDB entry 6i3j coloured by chain, side view.
PDB entry 6i3j coloured by chain, top view.
Source organism: Albifimbria verrucaria
Primary publication:
Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.
Kovaľ T, Švecová L, Østergaard LH, Skalova T, Dušková J, Hašek J, Kolenko P, Fejfarová K, Stránský J, Trundová M, Dohnálek J
OpenAccess logo Sci Rep 9 13700 (2019)
PMID: 31548583

Function and Biology Details

Reaction catalysed: 
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171387 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (5 distinct):
Bilirubin oxidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 534 amino acids
Theoretical weight: 60.01 KDa
Source organism: Albifimbria verrucaria
Expression system: Aspergillus oryzae
UniProt:
  • Canonical: Q12737 (Residues: 39-572; Coverage: 97%)
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
6 bound ligands:
Ligand CU 8 x CU
Ligand FC6 9 x FC6
Ligand SIN 5 x SIN
Ligand NA 8 x NA
Ligand CL 1 x CL
Ligand PGR 1 x PGR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: F222
Unit cell:
a: 134.382Å b: 203.846Å c: 226.744Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.16 0.226
Expression system: Aspergillus oryzae

Quick links

Citations

2 citation in other articles

Modelling covalent linkages in CCP4.
Nicholls et al. (2021)
1 more

3 mentions without citation

Paired refinement under the control of PAIREF.
Malý et al. (2020)
2 more