This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2dm5
From Proteopedia
| Line 4: | Line 4: | ||
|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> | ||
}} | }} | ||
| Line 28: | Line 31: | ||
[[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
| |||||||
| , 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
Page seeded by OCA on Mon Mar 31 02:36:28 2008
