2dm5: Difference between revisions
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[[Image:2dm5.gif|left|200px]] | [[Image:2dm5.gif|left|200px]] | ||
'''Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor''' | {{Structure | ||
|PDB= 2dm5 |SIZE=350|CAPTION= <scene name='initialview01'>2dm5</scene>, resolution 1.7Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> and <scene name='pdbligand=ODI:OCTANE-1,8-DIOL'>ODI</scene> | |||
|ACTIVITY= | |||
|GENE= MUP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]) | |||
}} | |||
'''Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2DM5 is a [ | 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== | ||
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:// | 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]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''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
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| 2dm5, resolution 1.7Å | |||||||||||||
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| Ligands: | CD and ODI | ||||||||||||
| 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
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