2sam

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[[Image:2sam.jpg|left|200px]]
 
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{{Structure
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==STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COMPLEX WITH AN IRREVERSIBLE NON-PEPTIDE INHIBITOR==
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|PDB= 2sam |SIZE=350|CAPTION= <scene name='initialview01'>2sam</scene>, resolution 2.4&Aring;
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<StructureSection load='2sam' size='340' side='right'caption='[[2sam]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=EPN:3-(4-NITRO-PHENOXY)-PROPAN-1-OL'>EPN</scene>
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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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|ACTIVITY=
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2sam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2sam OCA], [http://www.ebi.ac.uk/pdbsum/2sam PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2sam RCSB]</span>
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== Evolutionary Conservation ==
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}}
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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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==Overview==
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==See Also==
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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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*[[Immunodeficiency virus protease 3D structures|Immunodeficiency virus protease 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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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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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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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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[[Category: hydrolase(acid protease)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:02:47 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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