182l: Difference between revisions
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|PDB= 182l |SIZE=350|CAPTION= <scene name='initialview01'>182l</scene>, resolution 1.80Å | |PDB= 182l |SIZE=350|CAPTION= <scene name='initialview01'>182l</scene>, resolution 1.80Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=BZF:BENZOFURAN'>BZF</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=182l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=182l OCA], [http://www.ebi.ac.uk/pdbsum/182l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=182l RCSB]</span> | |||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
182L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | 182L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=182L OCA]. | ||
==Reference== | ==Reference== | ||
Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity., Morton A, Matthews BW, Biochemistry. 1995 Jul 11;34(27):8576-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7612599 7612599] | Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity., Morton A, Matthews BW, Biochemistry. 1995 Jul 11;34(27):8576-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7612599 7612599] | ||
[[Category: Enterobacteria phage | [[Category: Enterobacteria phage t4]] | ||
[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Matthews, B W.]] | [[Category: Matthews, B W.]] | ||
[[Category: Morton, A.]] | [[Category: Morton, A.]] | ||
[[Category: hydrolase (o-glycosyl)]] | [[Category: hydrolase (o-glycosyl)]] | ||
''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 18:29:31 2008'' | ||
Revision as of 18:29, 30 March 2008
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| , resolution 1.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Lysozyme, with EC number 3.2.1.17 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SPECIFICITY OF LIGAND BINDING IN A BURIED NON-POLAR CAVITY OF T4 LYSOZYME: LINKAGE OF DYNAMICS AND STRUCTURAL PLASTICITY
OverviewOverview
To better understand the role of shape complementarity in ligand binding and protein core interactions, the structures have been determined of a set of ligands bound within a cavity-containing mutant of T4 lysozyme. The interior cavity is seen to consist of two parts that respond very differently to the binding of ligands. First, there is a relatively rigid region that does not relax significantly upon binding any ligand. Second, there is a more flexible region that moves to various extents in response to binding the different ligands. The part of the binding site that remains rigid is characterized by low temperature factors and strong protection from hydrogen exchange. This part of the site appears to be primarily responsible for discriminating between ligands of different shape (i.e., for determining specificity). The more flexible region, characterized by relatively high temperature factors and weak protection from hydrogen exchange, allows some promiscuity in binding by undergoing variable amounts of deformation at essentially the same energetic cost. This linkage between the dynamic information represented by crystallographic temperature factors and hydrogen-exchange behavior on the one hand, and structural plasticity in response to ligand binding on the other hand, suggests a way to improve our understanding of steric interactions in protein cores and protein-ligand binding sites. Ligand design and packing algorithms might take advantage of this information, requiring complementary interactions where the protein is rigid and allowing some overlap in regions where the protein is flexible.
About this StructureAbout this Structure
182L is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
ReferenceReference
Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity., Morton A, Matthews BW, Biochemistry. 1995 Jul 11;34(27):8576-88. PMID:7612599
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