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2dm5

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[[Image:2dm5.gif|left|200px]]<br /><applet load="2dm5" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2dm5.gif|left|200px]]
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caption="2dm5, resolution 1.7&Aring;" />
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'''Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor'''<br />
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{{Structure
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|PDB= 2dm5 |SIZE=350|CAPTION= <scene name='initialview01'>2dm5</scene>, resolution 1.7&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> and <scene name='pdbligand=ODI:OCTANE-1,8-DIOL'>ODI</scene>
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|ACTIVITY=
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|GENE= MUP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
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}}
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'''Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2DM5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=CD:'>CD</scene> and <scene name='pdbligand=ODI:'>ODI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DM5 OCA].
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2DM5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DM5 OCA].
==Reference==
==Reference==
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Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor., Barratt E, Bronowska A, Vondrasek J, Cerny J, Bingham R, Phillips S, Homans SW, J Mol Biol. 2006 Oct 6;362(5):994-1003. Epub 2006 Aug 1. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16935302 16935302]
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Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor., Barratt E, Bronowska A, Vondrasek J, Cerny J, Bingham R, Phillips S, Homans SW, J Mol Biol. 2006 Oct 6;362(5):994-1003. Epub 2006 Aug 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16935302 16935302]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: lipocalin]]
[[Category: lipocalin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:00:14 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:28:50 2008''

Revision as of 14:28, 20 March 2008

Image:2dm5.gif


PDB ID 2dm5

Drag the structure with the mouse to rotate
, resolution 1.7Å
Ligands: and
Gene: MUP1 (Mus musculus)
Coordinates: save as pdb, mmCIF, xml



Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor


Overview

Here, we examine the thermodynamic penalty arising from burial of a polar group in a hydrophobic pocket that forms part of the binding-site of the major urinary protein (MUP-I). X-ray crystal structures of the complexes of octanol, nonanol and 1,8 octan-diol indicate that these ligands bind with similar orientations in the binding pocket. Each complex is characterised by a bridging water molecule between the hydroxyl group of Tyr120 and the hydroxyl group of each ligand. The additional hydroxyl group of 1,8 octan-diol is thereby forced to reside in a hydrophobic pocket, and isothermal titration calorimetry experiments indicate that this is accompanied by a standard free energy penalty of +21 kJ/mol with respect to octanol and +18 kJ/mol with respect to nonanol. Consideration of the solvation thermodynamics of each ligand enables the "intrinsic" (solute-solute) interaction energy to be determined, which indicates a favourable enthalpic component and an entropic component that is small or zero. These data indicate that the thermodynamic penalty to binding derived from the unfavourable desolvation of 1,8 octan-diol is partially offset by a favourable intrinsic contribution. Quantum chemical calculations suggest that this latter contribution derives from favourable solute-solute dispersion interactions.

About this Structure

2DM5 is a Single protein structure of sequence from Mus musculus. Full crystallographic information is available from OCA.

Reference

Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor., Barratt E, Bronowska A, Vondrasek J, Cerny J, Bingham R, Phillips S, Homans SW, J Mol Biol. 2006 Oct 6;362(5):994-1003. Epub 2006 Aug 1. PMID:16935302

Page seeded by OCA on Thu Mar 20 16:28:50 2008

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