› 2aqd

X-ray diffraction
1.35Å resolution

cytochrome c peroxidase (CCP) in complex with 2,5-diaminopyridine

Released:
DOI: 10.2210/pdb2aqd/pdb
PDB entry 2aqd coloured by chain, front view.
PDB entry 2aqd coloured by chain, side view.
PDB entry 2aqd coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Probing molecular docking in a charged model binding site.
Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK
J Mol Biol 357 1449-70 (2006)
PMID: 16490206

Function and Biology Details

Reaction catalysed: 
2 ferrocytochrome c + H(2)O(2) = 2 ferricytochrome c + 2 H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132475 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytochrome c peroxidase, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 294 amino acids
Theoretical weight: 33.46 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00431 (Residues: 71-361; Coverage: 81%)
Gene names: CCP, CCP1, CPO, YKR066C
Sequence domains: Peroxidase
Structure domains:

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM
1 bound ligand:
Ligand DA1 1 x DA1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 50.804Å b: 75.506Å c: 106.925Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.134 0.134 0.163
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".
Mobley et al. (2009)
3 more

1 mention without citation

Probing molecular docking in a charged model binding site.
Brenk et al. (2006)