1RYC

CYTOCHROME C PEROXIDASE W191G FROM SACCHAROMYCES CEREVISIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity.

Fitzgerald, M.M.Musah, R.A.McRee, D.E.Goodin, D.B.

(1996) Nat Struct Biol 3: 626-631

  • DOI: 10.1038/nsb0796-626
  • Primary Citation of Related Structures:  
    1AA4, 1AET, 1AES, 1AEU, 1CCI, 1RYC

  • PubMed Abstract: 
  • Conformational changes that gate the access of substrates or ligands to an active site are important features of enzyme function. In this report, we describe an unusual example of a structural rearrangement near a buried artificial cavity in cytochrome c peroxidase that occurs on binding protonated benzimidazole ...

    Conformational changes that gate the access of substrates or ligands to an active site are important features of enzyme function. In this report, we describe an unusual example of a structural rearrangement near a buried artificial cavity in cytochrome c peroxidase that occurs on binding protonated benzimidazole. A hinged main-chain rotation at two residues (Pro 190 and Asn 195) results in a surface loop rearrangement that opens a large solvent-accessible channel for the entry of ligands to an otherwise inaccessible binding site. The trapping of this alternate conformational state provides a unique view of the extent to which protein dynamics can allow small molecule penetration into buried protein cavities.


    Related Citations: 
    • The Role of Aspartate-235 in the Binding of Cations to an Artificial Cavity at the Radical Site of Cytochrome C Peroxidase
      Fitzgerald, M.M., Trester, M.L., Jensen, G.M., Mcree, D.E., Goodin, D.B.
      (1995) Protein Sci 4: 1844
    • Small Molecule Binding to an Artificially Created Cavity at the Active Site of Cytochrome C Peroxidase
      Fitzgerald, M.M., Churchill, M.J., Mcree, D.E., Goodin, D.B.
      (1994) Biochemistry 33: 3807
    • The Asp-His-Fe Triad of Cytochrome C Peroxidase Controls the Reduction Potential, Electronic Structure, and Coupling of the Tryptophan Free Radical to the Heme
      Goodin, D.B., Mcree, D.E.
      (1993) Biochemistry 32: 3313

    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C PEROXIDASE A294Saccharomyces cerevisiaeMutation(s): 1 
EC: 1.11.1.5
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BZI
Query on BZI

Download Ideal Coordinates CCD File 
A
BENZIMIDAZOLE
C7 H6 N2
HYZJCKYKOHLVJF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108α = 90
b = 77.3β = 90
c = 51.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other