4JM9

Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 3-amino-1-methylpyridinium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1016/j.jmb.2013.07.030
  • Primary Citation of Related Structures:  
    4JM5, 4JM6, 4JMA, 4JM8, 4JM9, 4JMW, 4JPT, 4JPU, 4JPL, 4JQK

  • 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 ...

    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.


    Related Citations: 
    • Docking to a water-filled model binding site in Cytochrome c Peroxidase
      Barelier, S., Boyce, S.E., Fischer, M., Fish, I., Goodin, D.B., Shoichet, B.K.
      () To be published --: --

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c peroxidaseA289Saccharomyces cerevisiae RM11-1aMutation(s): 2 
Gene Names: CCP1 CCP CPO YKR066CSCRG_04081
EC: 1.11.1.5 (PDB Primary Data), 1.11.1 (UniProt)
UniProt
Find proteins for B3LRE1 (Saccharomyces cerevisiae (strain RM11-1a))
Explore B3LRE1 
Go to UniProtKB:  B3LRE1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
D [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
LG5
Query on LG5

Download Ideal Coordinates CCD File 
C [auth A]1-METHYL-1,6-DIHYDROPYRIDIN-3-AMINE
C6 H10 N2
NJIDBKRVRJXCLL-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.026α = 90
b = 74.702β = 90
c = 106.585γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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