2sam

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{{Seed}}
 
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[[Image:2sam.png|left|200px]]
 
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==STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COMPLEX WITH AN IRREVERSIBLE NON-PEPTIDE INHIBITOR==
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The line below this paragraph, containing "STRUCTURE_2sam", creates the "Structure Box" on the page.
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<StructureSection load='2sam' size='340' side='right'caption='[[2sam]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2sam]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2SAM FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPN:3-(4-NITRO-PHENOXY)-PROPAN-1-OL'>EPN</scene></td></tr>
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{{STRUCTURE_2sam| PDB=2sam | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2sam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2sam OCA], [https://pdbe.org/2sam PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2sam RCSB], [https://www.ebi.ac.uk/pdbsum/2sam PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2sam ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sa/2sam_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2sam ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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A variant of the simian immunodeficiency virus protease (SIV PR), covalently bound to the inhibitor 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP), was crystallized. The structure of the inhibited complex was determined by X-ray crystallography to a resolution of 2.4 A and refined to an R factor of 19%. The variant, SIV PR S4H, was shown to diminish the rate of autolysis by at least 4-fold without affecting enzymatic parameters. The overall root mean square (rms) deviation of the alpha-carbons from the structure of HIV-1PR complexed with a peptidomimetic inhibitor (7HVP) was 1.16 A. The major differences are concentrated in three surface loops with rms differences between 1.2 and 2.1 A. For 60% of the molecule the rms deviation was only 0.6 A. The structure reveals one molecule of EPNP bound per protease dimer, a stoichiometry confirmed by mass spectral analysis. The epoxide moiety forms a covalent bond with either of the active site aspartic acids of the dimer, and the phenyl moiety occupies the P1 binding site. The EPNP nitro group interacts with Arg 8. This structure suggests a starting template for the design of nonpeptide-based irreversible inhibitors of the SIV and related HIV-1 and HIV-2 PRs.
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===STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COMPLEX WITH AN IRREVERSIBLE NON-PEPTIDE INHIBITOR===
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Structure of the protease from simian immunodeficiency virus: complex with an irreversible nonpeptide inhibitor.,Rose RB, Rose JR, Salto R, Craik CS, Stroud RM Biochemistry. 1993 Nov 23;32(46):12498-507. PMID:8241141<ref>PMID:8241141</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2sam" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_8241141}}, adds the Publication Abstract to the page
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*[[Immunodeficiency virus protease 3D structures|Immunodeficiency virus protease 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 8241141 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_8241141}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2SAM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SAM OCA].
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==Reference==
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Structure of the protease from simian immunodeficiency virus: complex with an irreversible nonpeptide inhibitor., Rose RB, Rose JR, Salto R, Craik CS, Stroud RM, Biochemistry. 1993 Nov 23;32(46):12498-507. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8241141 8241141]
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[[Category: Simian immunodeficiency virus]]
[[Category: Simian immunodeficiency virus]]
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[[Category: Single protein]]
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[[Category: Craik CS]]
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[[Category: Craik, C S.]]
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[[Category: Rose JR]]
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[[Category: Rose, J R.]]
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[[Category: Rose RB]]
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[[Category: Rose, R B.]]
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[[Category: Salto R]]
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[[Category: Salto, R.]]
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[[Category: Stroud RM]]
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[[Category: Stroud, R M.]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 12:29:38 2008''
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Current revision

STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COMPLEX WITH AN IRREVERSIBLE NON-PEPTIDE INHIBITOR

PDB ID 2sam

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