› 2rbx

X-ray diffraction
1.5Å resolution

Cytochrome C Peroxidase W191G in complex with pyrimidine-2,4,6-triamine.

Released:
DOI: 10.2210/pdb2rbx/pdb
PDB entry 2rbx coloured by chain, front view.
PDB entry 2rbx coloured by chain, side view.
PDB entry 2rbx coloured by chain, top view.
Source organism: Saccharomyces cerevisiae YJM789
Primary publication:
Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK
J Mol Biol 377 914-34 (2008)
PMID: 18280498

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: X
Molecule details ›
Chain: X
Length: 292 amino acids
Theoretical weight: 33.2 KDa
Source organism: Saccharomyces cerevisiae YJM789
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
2 bound ligands:
Ligand PO4 1 x PO4
Ligand 3AY 1 x 3AY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 50.923Å b: 75.141Å c: 107.051Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.152 0.173
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

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

1 mention without citation

Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
Graves et al. (2008)