1CCJ

CONFORMER SELECTION BY LIGAND BINDING OBSERVED WITH PROTEIN CRYSTALLOGRAPHY


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

Protein conformer selection by ligand binding observed with crystallography.

Cao, Y.Musah, R.A.Wilcox, S.K.Goodin, D.B.McRee, D.E.

(1998) Protein Sci. 7: 72-78

  • DOI: 10.1002/pro.5560070107

  • PubMed Abstract: 
  • A large-scale movement between "closed" and "open" conformations of a protein loop was observed directly with protein crystallography by trapping individual conformers through binding of an exogenous ligand and characterization with solution kinetics ...

    A large-scale movement between "closed" and "open" conformations of a protein loop was observed directly with protein crystallography by trapping individual conformers through binding of an exogenous ligand and characterization with solution kinetics. The buried indole ring of Trp191 in cytochrome c peroxidase (CCP) was displaced by exogenous ligands, causing a conformational change of loop Pro190-Asn195 and exposing Trp191 to the protein surface. Kinetic measurements are consistent with a two-step binding mechanism in which the rate-limiting step is a transition of the protein to the open state, which then binds the ligand. This large-scale conformational change of a functionally important region of CCP is independent of ligand and indicates that about 4% of the wild-type protein is in the open form in solution at any given time.


    Related Citations: 
    • 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, The 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)Mutation(s): 1 
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 1 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
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 = 108.300α = 90.00
b = 77.140β = 90.00
c = 51.720γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
XENGENdata reduction
X-PLORphasing
XENGENdata scaling
XTALVIEWrefinement
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance