4XV5

CcP gateless cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.

Fischer, M.Shoichet, B.K.Fraser, J.S.

(2015) Chembiochem 16: 1560-1564

  • DOI: 10.1002/cbic.201500196
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Interrogating fragment libraries by X-ray crystallography is a powerful strategy for discovering allosteric ligands for protein targets. Cryocooling of crystals should theoretically increase the fraction of occupied binding sites and decrease radiati ...

    Interrogating fragment libraries by X-ray crystallography is a powerful strategy for discovering allosteric ligands for protein targets. Cryocooling of crystals should theoretically increase the fraction of occupied binding sites and decrease radiation damage. However, it might also perturb protein conformations that can be accessed at room temperature. Using data from crystals measured consecutively at room temperature and at cryogenic temperature, we found that transient binding sites could be abolished at the cryogenic temperatures employed by standard approaches. Changing the temperature at which the crystallographic data was collected could provide a deliberate perturbation to the equilibrium of protein conformations and help to visualize hidden sites with great potential to allosterically modulate protein function.


    Related Citations: 
    • Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
      Fischer, M.,Coleman, R.G.,Fraser, J.S.,Shoichet, B.K.
      (2014) Nat Chem 6: 575


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., Byers Hall, BH-501, Box 2550, San Francisco, CA 94158 (USA).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c peroxidase, mitochondrial
A
292Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
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
BZI
Query on BZI

Download SDF File 
Download CCD File 
A
BENZIMIDAZOLE
C7 H6 N2
HYZJCKYKOHLVJF-UHFFFAOYSA-N
 Ligand Interaction
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: 1.65 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.113 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.530α = 90.00
b = 76.830β = 90.00
c = 107.570γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM59957
National Institutes of Health/Office of the DirectorUnited StatesOD009180
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM110580
National Science Foundation (United States)United StatesSTC-1231306

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-06-24
    Type: Database references
  • Version 1.2: 2015-07-29
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Source and taxonomy