4XV4

CcP gateless cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.112 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    4XVA, 4XV4, 4XV5, 4XV6, 4XV7, 4XV8

  • 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 radiation damage ...

    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 Bioengineering and Therapeutic Sciences, University of California San Francisco, 600 16th St., Genentech Hall, S472E, Box 2240, San Francisco, CA 94158 (USA). james.fraser@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c peroxidase, mitochondrialA289Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: CCP1CCPCPOYKR066C
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 CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
25T
Query on 25T

Download CCD File 
A
2-AMINO-5-METHYLTHIAZOLE
C4 H7 N2 S
GUABFMPMKJGSBQ-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
25TKd:  68000000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.112 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.53α = 90
b = 76.52β = 90
c = 107.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2015-07-29
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence