2dm5
From Proteopedia
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|PDB= 2dm5 |SIZE=350|CAPTION= <scene name='initialview01'>2dm5</scene>, resolution 1.7Å | |PDB= 2dm5 |SIZE=350|CAPTION= <scene name='initialview01'>2dm5</scene>, resolution 1.7Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> | + | |LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=ODI:OCTANE-1,8-DIOL'>ODI</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= MUP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]) | |GENE= MUP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dm5 OCA], [http://www.ebi.ac.uk/pdbsum/2dm5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dm5 RCSB]</span> | ||
}} | }} | ||
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[[Category: Phillips, S.]] | [[Category: Phillips, S.]] | ||
[[Category: Vondrasek, J.]] | [[Category: Vondrasek, J.]] | ||
| - | [[Category: CD]] | ||
| - | [[Category: ODI]] | ||
[[Category: beta barrel]] | [[Category: beta barrel]] | ||
[[Category: lipocalin]] | [[Category: lipocalin]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:36:28 2008'' |
Revision as of 23:36, 30 March 2008
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| , resolution 1.7Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | MUP1 (Mus musculus) | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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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