1b4h: Difference between revisions
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|PDB= 1b4h |SIZE=350|CAPTION= <scene name='initialview01'>1b4h</scene>, resolution 1.9Å | |PDB= 1b4h |SIZE=350|CAPTION= <scene name='initialview01'>1b4h</scene>, resolution 1.9Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=U1:URANIUM ATOM'>U1</scene> | |LIGAND= <scene name='pdbligand=DAB:2,4-DIAMINOBUTYRIC+ACID'>DAB</scene>, <scene name='pdbligand=U1:URANIUM+ATOM'>U1</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4h OCA], [http://www.ebi.ac.uk/pdbsum/1b4h PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b4h RCSB]</span> | |||
}} | }} | ||
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[[Category: Davies, T G.]] | [[Category: Davies, T G.]] | ||
[[Category: Tame, J R.H.]] | [[Category: Tame, J R.H.]] | ||
[[Category: periplasmic peptide binding protein]] | [[Category: periplasmic peptide binding protein]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:53:29 2008'' | ||
Revision as of 18:53, 30 March 2008
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| , resolution 1.9Å | |||||||
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| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-DIAMINOBUTYRIC ACID-LYSINE
OverviewOverview
The oligopeptide-binding protein OppA provides a useful model system for studying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X-ray crystallography. The tripeptides fall into three series of ligands, which have been designed to examine the effects of small changes to the central side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly due to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is proposed to arise from unfavorable electrostatic interactions in the pocket, including the disruption of a key salt bridge. Marked entropy-enthalpy compensation is found across the series, and some of the difficulties in designing tightly binding ligands have been highlighted.
About this StructureAbout this Structure
1B4H is a Single protein structure of sequence from Salmonella typhimurium. Full crystallographic information is available from OCA.
ReferenceReference
Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes., Davies TG, Hubbard RE, Tame JR, Protein Sci. 1999 Jul;8(7):1432-44. PMID:10422831
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