1AES

SPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACTIVE SITE OF CYTOCHROME C PEROXIDASE (IMIDAZOLE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 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.Mol.Biol. 3: 626-631

  • Primary Citation of Related Structures:  1AA4, 1AET, 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 cytochro ...

    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 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C PEROXIDASE
A
294Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CCP1 (CCP, CPO)
EC: 1.11.1.5
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00431
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 108.000α = 90.00
b = 77.300β = 90.00
c = 51.800γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
XTALVIEWrefinement
XENGENdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance