› 2rbt

X-ray diffraction
1.24Å resolution

n-methylbenzylamine in complex with Cytochrome C Peroxidase W191G

Released:
DOI: 10.2210/pdb2rbt/pdb
PDB entry 2rbt coloured by chain, front view.
PDB entry 2rbt coloured by chain, side view.
PDB entry 2rbt 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
3 bound ligands:
Ligand PO4 1 x PO4
Ligand 271 1 x 271
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P212121
Unit cell:
a: 50.989Å b: 75.752Å c: 107.08Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.123 0.122 0.146
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)