1nkm

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{{Seed}}
 
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[[Image:1nkm.png|left|200px]]
 
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==Complex structure of HCMV Protease and a peptidomimetic inhibitor==
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The line below this paragraph, containing "STRUCTURE_1nkm", creates the "Structure Box" on the page.
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<StructureSection load='1nkm' size='340' side='right'caption='[[1nkm]], [[Resolution|resolution]] 2.70&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'>[[1nkm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_betaherpesvirus_5 Human betaherpesvirus 5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NKM 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]] 2.7&#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=0FP:N-(6-AMINOHEXANOYL)-3-METHYL-L-VALYL-3-METHYL-L-VALYL-N~1~-[(2S,3S)-3-HYDROXY-4-OXO-4-{[(1R)-1-PHENYLPROPYL]AMINO}BUTAN-2-YL]-N~4~,N~4~-DIMETHYL-L-ASPARTAMIDE'>0FP</scene></td></tr>
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{{STRUCTURE_1nkm| PDB=1nkm | 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=1nkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkm OCA], [https://pdbe.org/1nkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nkm RCSB], [https://www.ebi.ac.uk/pdbsum/1nkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkm ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SCAF_HCMVA SCAF_HCMVA] Capsid scaffolding protein acts as a scaffold protein by binding major capsid protein UL86 in the cytoplasm, inducing the nuclear localization of both proteins. Multimerizes in the nucleus such as protein UL86 forms the icosahedral T=16 capsid. Autocatalytic cleavage releases the assembly protein, and subsequently abolishes interaction with major capsid protein UL86. Cleavages products are evicted from the capsid before or during DNA packaging (By similarity). Assemblin is a protease essential for virion assembly in the nucleus. Catalyzes the cleavage of the assembly protein after complete capsid formation. Assemblin and cleavages products are evicted from the capsid before or during DNA packaging (By similarity). Assembly protein plays a major role in capsid assembly. Acts as a scaffold protein by binding major capsid protein UL86. Multimerizes in the nucleus such as protein UL86 forms the icosahedral T=16 capsid. Cleaved by assemblin after capsid completion. The cleavages products are evicted from the capsid before or during DNA packaging (By similarity).
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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/nk/1nkm_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=1nkm 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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Herpesvirus protease is required for the life cycle of the virus and is an attractive target for the design and development of new anti-herpes agents. The protease belongs to a new class of serine proteases, with a novel backbone fold and a unique Ser-His-His catalytic triad. Here we report the crystal structures of human cytomegalovirus protease in complex with two peptidomimetic inhibitors. The structures reveal a new hydrogen-bonding interaction between the main chain carbonyl of the P(5) residue and the main chain amide of amino acid 137 of the protease, which is important for the binding affinity of the inhibitor. Conformational flexibility was observed in the S(3) pocket of the enzyme, and this is supported by our characterization of several mutants in this pocket. One of the structures is at 2.5 A resolution, allowing us for the first time to locate ordered solvent molecules in the inhibitor complex. The presence of two solvent molecules in the active site may have implications for the design of new inhibitors against this enzyme. Favorable and stereospecific interactions have been established in the S(1)' pocket for one of these inhibitors.
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===COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR===
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Structural and biochemical studies of inhibitor binding to human cytomegalovirus protease.,Khayat R, Batra R, Qian C, Halmos T, Bailey M, Tong L Biochemistry. 2003 Feb 4;42(4):885-91. PMID:12549906<ref>PMID:12549906</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 1nkm" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_12549906}}, adds the Publication Abstract to the page
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*[[Virus protease 3D structures|Virus protease 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 12549906 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12549906}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Human betaherpesvirus 5]]
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1NKM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_5 Human herpesvirus 5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKM OCA].
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[[Category: Large Structures]]
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[[Category: Bailey M]]
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==Reference==
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[[Category: Batra R]]
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Structural and biochemical studies of inhibitor binding to human cytomegalovirus protease., Khayat R, Batra R, Qian C, Halmos T, Bailey M, Tong L, Biochemistry. 2003 Feb 4;42(4):885-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12549906 12549906]
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[[Category: Halmos T]]
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[[Category: Assemblin]]
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[[Category: Khayat R]]
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[[Category: Human herpesvirus 5]]
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[[Category: Qian C]]
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[[Category: Single protein]]
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[[Category: Tong L]]
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[[Category: Bailey, M.]]
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[[Category: Batra, R.]]
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[[Category: Halmos, T.]]
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[[Category: Khayat, R.]]
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[[Category: Qian, C.]]
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[[Category: Tong, L.]]
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[[Category: Hydrolase]]
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[[Category: Induced-fit]]
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[[Category: Peptidomimetic inhibitor]]
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[[Category: Protease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:50:52 2008''
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Current revision

Complex structure of HCMV Protease and a peptidomimetic inhibitor

PDB ID 1nkm

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