4JM8

Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 2,6-diaminopyridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Blind prediction of charged ligand binding affinities in a model binding site.

Rocklin, G.J.Boyce, S.E.Fischer, M.Fish, I.Mobley, D.L.Shoichet, B.K.Dill, K.A.

(2013) J Mol Biol 425: 4569-4583

  • DOI: https://doi.org/10.1016/j.jmb.2013.07.030
  • Primary Citation of Related Structures:  
    4JM5, 4JM6, 4JM8, 4JM9, 4JMA, 4JMW, 4JPL, 4JPT, 4JPU, 4JQJ, 4JQK, 4JQM, 4JQN

  • PubMed Abstract: 

    Predicting absolute protein-ligand binding affinities remains a frontier challenge in ligand discovery and design. This becomes more difficult when ionic interactions are involved because of the large opposing solvation and electrostatic attraction energies. In a blind test, we examined whether alchemical free-energy calculations could predict binding affinities of 14 charged and 5 neutral compounds previously untested as ligands for a cavity binding site in cytochrome c peroxidase. In this simplified site, polar and cationic ligands compete with solvent to interact with a buried aspartate. Predictions were tested by calorimetry, spectroscopy, and crystallography. Of the 15 compounds predicted to bind, 13 were experimentally confirmed, while 4 compounds were false negative predictions. Predictions had a root-mean-square error of 1.95 kcal/mol to the experimental affinities, and predicted poses had an average RMSD of 1.7Å to the crystallographic poses. This test serves as a benchmark for these thermodynamically rigorous calculations at predicting binding affinities for charged compounds and gives insights into the existing sources of error, which are primarily electrostatic interactions inside proteins. Our experiments also provide a useful set of ionic binding affinities in a simplified system for testing new affinity prediction methods.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2550, USA; Biophysics Graduate Program, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2550, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c peroxidase289Saccharomyces cerevisiae RM11-1aMutation(s): 2 
Gene Names: CCP1 CCP CPO YKR066CSCRG_04081
EC: 1.11.1.5
UniProt
Find proteins for B3LRE1 (Saccharomyces cerevisiae (strain RM11-1a))
Explore B3LRE1 
Go to UniProtKB:  B3LRE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3LRE1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.843α = 90
b = 74.519β = 90
c = 106.464γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations