1rrl

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{{STRUCTURE_1rrl| PDB=1rrl | SCENE= }}
{{STRUCTURE_1rrl| PDB=1rrl | SCENE= }}
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'''Soybean Lipoxygenase (LOX-3) at 93K at 2.0 A resolution'''
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===Soybean Lipoxygenase (LOX-3) at 93K at 2.0 A resolution===
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==Overview==
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Flash-freezing is a technique that is commonly used nowadays to collect diffraction data for X-ray structural analysis. It can affect both the crystal and molecular structure and the molecule's surface, as well as the internal cavities. X-ray structural data often serve as a template for the protein receptor in docking calculations. Thus, the size and shape of the binding site determines which small molecules could be found as potential ligands in silico, especially during high-throughput rigid docking. Data were analyzed for wild soybean lipoxygenase-3 (MW 97 kDa) at 293 and 93 K and compared with the results from studies of its molecular complexes with known inhibitors, structures published by others for a derivative of the same enzyme (98 K) or a topologically close isozyme lipoxygenase-1 (at ambient temperature and 100 K). Analysis of these data allows the following conclusions. (i) Very small changes in the relative orientation of the molecules in the crystal can cause major changes in the crystal reciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing even when the unit-cell and the protein molecular volume show changes of only 1-2%. (iii) Using a receptor structure determined based on cryogenic data as a target for computational screening requires flexible docking to enable the expansion of the binding-site cavity and sampling of the alternative conformations of the crucial residues.
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(as it appears on PubMed at http://www.pubmed.gov), where 16790932 is the PubMed ID number.
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{{ABSTRACT_PUBMED_16790932}}
==About this Structure==
==About this Structure==
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[[Category: Lipoxygenase]]
[[Category: Lipoxygenase]]
[[Category: Oxidoreductase]]
[[Category: Oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:49:45 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:41:33 2008''

Revision as of 00:41, 29 July 2008

Image:1rrl.png

Template:STRUCTURE 1rrl

Soybean Lipoxygenase (LOX-3) at 93K at 2.0 A resolution

Template:ABSTRACT PUBMED 16790932

About this Structure

1RRL is a Single protein structure of sequence from Glycine max. Full crystallographic information is available from OCA.

Reference

Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution., Skrzypczak-Jankun E, Borbulevych OY, Zavodszky MI, Baranski MR, Padmanabhan K, Petricek V, Jankun J, Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):766-75. Epub 2006, Jun 20. PMID:16790932

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