1ZND

Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex.

Malham, R.Johnstone, S.Bingham, R.J.Barratt, E.Phillips, S.E.Laughton, C.A.Homans, S.W.

(2005) J.Am.Chem.Soc. 127: 17061-17067

  • DOI: 10.1021/ja055454g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The contributions of solute-solute dispersion interactions to binding thermodynamics have generally been thought to be small, due to the surmised equality between solute-solvent dispersion interactions prior to the interaction versus solute-solute di ...

    The contributions of solute-solute dispersion interactions to binding thermodynamics have generally been thought to be small, due to the surmised equality between solute-solvent dispersion interactions prior to the interaction versus solute-solute dispersion interactions following the interaction. The thermodynamics of binding of primary alcohols to the major urinary protein (MUP-I) indicate that this general assumption is not justified. The enthalpy of binding becomes more favorable with increasing chain length, whereas the entropy of binding becomes less favorable, both parameters showing a linear dependence. Despite the hydrophobicity of the interacting species, these data show that binding is not dominated by the classical hydrophobic effect, but can be attributed to favorable ligand-protein dispersion interactions.


    Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Biochemistry & Molecular Biology, University of Leeds, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major Urinary Protein
A
174Mus musculusMutation(s): 0 
Gene Names: Mup2
Find proteins for P11589 (Mus musculus)
Go to UniProtKB:  P11589
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE9
Query on PE9

Download SDF File 
Download CCD File 
A
PENTAN-1-OL
C5 H12 O
AMQJEAYHLZJPGS-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PE9ΔG: -17.2 - -33.9 kJ/mol (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.511α = 90.00
b = 53.511β = 90.00
c = 136.974γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance