9hvp - Revision history

OCA at 09:45, 14 February 2024

OCA — Wed, 14 Feb 2024 09:45:23 GMT

←Older revision		Revision as of 09:45, 14 February 2024
Line 1:		Line 1:

	==Design, activity and 2.8 Angstroms crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease==		==Design, activity and 2.8 Angstroms crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease==
-	<StructureSection load='9hvp' size='340' side='right' caption='[[9hvp]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='9hvp' size='340' side='right'caption='[[9hvp]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[9hvp]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=9HVP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[9hvp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9HVP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0E9:BENZYL+[(1R,4S,6S,9R)-4,6-DIBENZYL-5-HYDROXY-1,9-BIS(1-METHYLETHYL)-2,8,11-TRIOXO-13-PHENYL-12-OXA-3,7,10-TRIAZATRIDEC-1-YL]CARBAMATE'>0E9</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.8Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [~~http~~://pdbe.org/9hvp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/9hvp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=9hvp ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0E9:BENZYL+[(1R,4S,6S,9R)-4,6-DIBENZYL-5-HYDROXY-1,9-BIS(1-METHYLETHYL)-2,8,11-TRIOXO-13-PHENYL-12-OXA-3,7,10-TRIAZATRIDEC-1-YL]CARBAMATE'>0E9</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [https://pdbe.org/9hvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB], [https://www.ebi.ac.uk/pdbsum/9hvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9hvp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/POL_HV1N5 POL_HV1N5] Gag-Pol polyprotein and Gag polyprotein may regulate their own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, Gag-Pol and Gag would promote translation, whereas at high concentration, the polyproteins encapsidate genomic RNA and then shutt off translation (By similarity). Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. The second function is to play a role in nuclear localization of the viral genome at the very start of cell infection. Matrix protein is the part of the pre-integration complex. It binds in the cytoplasm the human BAF protein which prevent autointegration of the viral genome, and might be included in virions at the ration of zero to 3 BAF dimer per virion. The myristoylation signal and the NLS thus exert conflicting influences its subcellular localization. The key regulation of these motifs might be phosphorylation of a portion of MA molecules on the C-terminal tyrosine at the time of virus maturation, by virion-associated cellular tyrosine kinase. Implicated in the release from host cell mediated by Vpu (By similarity). Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is disassembled soon after virion entry. Interaction with human PPIA/CYPA protects the virus from restriction by human TRIM5-alpha and from an unknown antiviral activity in human cells. This capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species (By similarity). Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. This capability is referred to as nucleic acid chaperone activity (By similarity). The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. Also cleaves Nef and Vif, probably concomitantly with viral structural proteins on maturation of virus particles (By similarity). Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA(3)-Lys binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for two polypurine tracts (PPTs) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPTs that have not been removed by RNase H as primers. PPTs and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hv/9hvp_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hv/9hvp_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 17:		Line 20:
	</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=9hvp ConSurf].		</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=9hvp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A two-fold (C2) symmetric inhibitor of the protease of human immunodeficiency virus type-1 (HIV-1) has been designed on the basis of the three-dimensional symmetry of the enzyme active site. The symmetric molecule inhibited both protease activity and acute HIV-1 infection in vitro, was at least 10,000-fold more potent against HIV-1 protease than against related enzymes, and appeared to be stable to degradative enzymes. The 2.8 angstrom crystal structure of the inhibitor-enzyme complex demonstrated that the inhibitor binds to the enzyme in a highly symmetric fashion.

-	Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease.,Erickson J, Neidhart DJ, VanDrie J, Kempf DJ, Wang XC, Norbeck DW, Plattner JJ, Rittenhouse JW, Turon M, Wideburg N, et al. Science. 1990 Aug 3;249(4968):527-33. PMID:2200122<ref>PMID:2200122</ref>	+	==See Also==
-		+	*[[Immunodeficiency virus protease 3D structures\|Immunodeficiency virus protease 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 9hvp" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Erickson, J~~]]	+	[[Category: Human immunodeficiency virus 1]]
-	[[Category: ~~Neidhart, D J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Acid proteinase~~]]	+	[[Category: Erickson J]]
-	[[Category: ~~Hydrolase-hydrolase inhibitor complex~~]]	+	[[Category: Neidhart DJ]]

OCA at 16:27, 11 August 2016

OCA — Thu, 11 Aug 2016 16:27:07 GMT

←Older revision		Revision as of 16:27, 11 August 2016
Line 1:		Line 1:
		+
	==Design, activity and 2.8 Angstroms crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease==		==Design, activity and 2.8 Angstroms crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease==
	<StructureSection load='9hvp' size='340' side='right' caption='[[9hvp]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='9hvp' size='340' side='right' caption='[[9hvp]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[9hvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_immunodeficiency_virus_1 Human immunodeficiency virus 1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9HVP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[9hvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9HVP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0E9:BENZYL+[(1R,4S,6S,9R)-4,6-DIBENZYL-5-HYDROXY-1,9-BIS(1-METHYLETHYL)-2,8,11-TRIOXO-13-PHENYL-12-OXA-3,7,10-TRIAZATRIDEC-1-YL]CARBAMATE'>0E9</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0E9:BENZYL+[(1R,4S,6S,9R)-4,6-DIBENZYL-5-HYDROXY-1,9-BIS(1-METHYLETHYL)-2,8,11-TRIOXO-13-PHENYL-12-OXA-3,7,10-TRIAZATRIDEC-1-YL]CARBAMATE'>0E9</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB], [http://www.ebi.ac.uk/pdbsum/9hvp PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [http://pdbe.org/9hvp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB], [http://www.ebi.ac.uk/pdbsum/9hvp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=9hvp ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=9hvp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 9hvp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human immunodeficiency virus 1]]
	[[Category: Erickson, J]]		[[Category: Erickson, J]]
	[[Category: Neidhart, D J]]		[[Category: Neidhart, D J]]
	[[Category: Acid proteinase]]		[[Category: Acid proteinase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 08:56, 5 January 2015

OCA — Mon, 05 Jan 2015 08:56:53 GMT

←Older revision		Revision as of 08:56, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[9hvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9HVP FirstGlance]. <br>		<table><tr><td colspan='2'>[[9hvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9HVP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0E9:BENZYL+[(1R,4S,6S,9R)-4,6-DIBENZYL-5-HYDROXY-1,9-BIS(1-METHYLETHYL)-2,8,11-TRIOXO-13-PHENYL-12-OXA-3,7,10-TRIAZATRIDEC-1-YL]CARBAMATE'>0E9</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0E9:BENZYL+[(1R,4S,6S,9R)-4,6-DIBENZYL-5-HYDROXY-1,9-BIS(1-METHYLETHYL)-2,8,11-TRIOXO-13-PHENYL-12-OXA-3,7,10-TRIAZATRIDEC-1-YL]CARBAMATE'>0E9</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB], [http://www.ebi.ac.uk/pdbsum/9hvp PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB], [http://www.ebi.ac.uk/pdbsum/9hvp PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
-	[[Category: Erickson, J.]]	+	[[Category: Erickson, J]]
-	[[Category: Neidhart, D J.]]	+	[[Category: Neidhart, D J]]
	[[Category: Acid proteinase]]		[[Category: Acid proteinase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA: Protected "9hvp" [edit=sysop:move=sysop]

OCA — Thu, 05 Jun 2014 09:17:44 GMT

Protected "9hvp" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:17, 5 June 2014

OCA at 09:17, 5 June 2014

OCA — Thu, 05 Jun 2014 09:17:42 GMT

←Older revision		Revision as of 09:17, 5 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==Design, activity and 2.8 Angstroms crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease==
-	[[~~Image~~:9hvp.~~png\|left~~\|200px]]	+	<StructureSection load='9hvp' size='340' side='right' caption='[[9hvp]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[9hvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9HVP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0E9:BENZYL+[(1R,4S,6S,9R)-4,6-DIBENZYL-5-HYDROXY-1,9-BIS(1-METHYLETHYL)-2,8,11-TRIOXO-13-PHENYL-12-OXA-3,7,10-TRIAZATRIDEC-1-YL]CARBAMATE'>0E9</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB], [http://www.ebi.ac.uk/pdbsum/9hvp PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hv/9hvp_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A two-fold (C2) symmetric inhibitor of the protease of human immunodeficiency virus type-1 (HIV-1) has been designed on the basis of the three-dimensional symmetry of the enzyme active site. The symmetric molecule inhibited both protease activity and acute HIV-1 infection in vitro, was at least 10,000-fold more potent against HIV-1 protease than against related enzymes, and appeared to be stable to degradative enzymes. The 2.8 angstrom crystal structure of the inhibitor-enzyme complex demonstrated that the inhibitor binds to the enzyme in a highly symmetric fashion.

-	<!--	+	Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease.,Erickson J, Neidhart DJ, VanDrie J, Kempf DJ, Wang XC, Norbeck DW, Plattner JJ, Rittenhouse JW, Turon M, Wideburg N, et al. Science. 1990 Aug 3;249(4968):527-33. PMID:2200122<ref>PMID:2200122</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_9hvp"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_9hvp\| PDB=9hvp \| SCENE= }}~~	+

-	~~===DESIGN~~, ~~ACTIVITY AND 2.8 ANGSTROMS CRYSTAL STRUCTURE OF A C2 SYMMETRIC INHIBITOR COMPLEXED TO HIV-1 PROTEASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_2200122}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 2200122 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_2200122}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~9HVP is a 2 chains structure of sequences from [http:~~/~~/en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:2200122<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Erickson, J.]]		[[Category: Erickson, J.]]
	[[Category: Neidhart, D J.]]		[[Category: Neidhart, D J.]]
-		+	[[Category: Acid proteinase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 05~~:~~52:49 2009''~~	+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 03:52, 18 February 2009

OCA — Wed, 18 Feb 2009 03:52:51 GMT

←Older revision		Revision as of 03:52, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	9HVP is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA].	+	9HVP is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA].

	==Reference==		==Reference==
-	Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease., Erickson J, Neidhart DJ, VanDrie J, Kempf DJ, Wang XC, Norbeck DW, Plattner JJ, Rittenhouse JW, Turon M, Wideburg N, et al., Science. 1990 Aug 3;249(4968):527-33. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/2200122 2200122]~~	+	<ref group="xtra">PMID:2200122</ref><references group="xtra"/>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
-	[[Category: Single protein]]
	[[Category: Erickson, J.]]		[[Category: Erickson, J.]]
	[[Category: Neidhart, D J.]]		[[Category: Neidhart, D J.]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri Jul 11 12~~:55:~~46 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:52:49 2009''

OCA at 09:55, 11 July 2008

OCA — Fri, 11 Jul 2008 09:55:46 GMT

←Older revision		Revision as of 09:55, 11 July 2008
Line 1:		Line 1:
-	[[Image:9hvp.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:9hvp.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_9hvp\| PDB=9hvp \| SCENE= }}		{{STRUCTURE_9hvp\| PDB=9hvp \| SCENE= }}

-	~~'''~~DESIGN, ACTIVITY AND 2.8 ANGSTROMS CRYSTAL STRUCTURE OF A C2 SYMMETRIC INHIBITOR COMPLEXED TO HIV-1 PROTEASE~~'''~~	+	===DESIGN, ACTIVITY AND 2.8 ANGSTROMS CRYSTAL STRUCTURE OF A C2 SYMMETRIC INHIBITOR COMPLEXED TO HIV-1 PROTEASE===


-	~~==Overview==~~	+	<!--
-	~~A two~~-~~fold (C2) symmetric inhibitor of the protease of human immunodeficiency virus type~~-~~1 (HIV-1) has been designed on the basis of the three-dimensional symmetry of the enzyme active site.~~ The ~~symmetric molecule inhibited both protease activity and acute HIV-1 infection in vitro~~, ~~was at least 10~~,~~000-fold more potent against HIV-1 protease than against related enzymes, and appeared~~ to ~~be stable to degradative enzymes~~. ~~The 2~~.~~8 angstrom crystal structure of~~ the ~~inhibitor~~-~~enzyme complex demonstrated that the inhibitor binds to the enzyme in a highly symmetric fashion.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_2200122}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 2200122 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_2200122}}

	==About this Structure==		==About this Structure==
Line 24:		Line 28:
	[[Category: Erickson, J.]]		[[Category: Erickson, J.]]
	[[Category: Neidhart, D J.]]		[[Category: Neidhart, D J.]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 22~~:53:07 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Jul 11 12:55:46 2008''

OCA at 19:53, 4 May 2008

OCA — Sun, 04 May 2008 19:53:08 GMT

←Older revision		Revision as of 19:53, 4 May 2008
Line 1:		Line 1:
	[[Image:9hvp.gif\|left\|200px]]		[[Image:9hvp.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 9hvp \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>9hvp</scene>~~, ~~resolution 2~~.~~8Å~~	+	The line below this paragraph, containing "STRUCTURE_9hvp", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=COR:2,4~~-~~DIAMINO~~-~~1,5-DIPHENYL-3-HYDROXYPENTANE'>COR</scene>, <scene name='pdbligand=PHQ:FORMIC+ACID+BENZYL+ESTER'>PHQ</scene~~>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_9hvp\| PDB=9hvp \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [http://www.ebi.ac.uk/pdbsum/9hvp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB]</span>	+
-	}}	+

	'''DESIGN, ACTIVITY AND 2.8 ANGSTROMS CRYSTAL STRUCTURE OF A C2 SYMMETRIC INHIBITOR COMPLEXED TO HIV-1 PROTEASE'''		'''DESIGN, ACTIVITY AND 2.8 ANGSTROMS CRYSTAL STRUCTURE OF A C2 SYMMETRIC INHIBITOR COMPLEXED TO HIV-1 PROTEASE'''
Line 27:		Line 24:
	[[Category: Erickson, J.]]		[[Category: Erickson, J.]]
	[[Category: Neidhart, D J.]]		[[Category: Neidhart, D J.]]
-	~~[[Category: hydrolase(acid proteinase)]]~~	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:53:07 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:46:07 2008''	+

OCA at 02:46, 31 March 2008

OCA — Mon, 31 Mar 2008 02:46:07 GMT

←Older revision		Revision as of 02:46, 31 March 2008
Line 4:		Line 4:
	\|PDB= 9hvp \|SIZE=350\|CAPTION= <scene name='initialview01'>9hvp</scene>, resolution 2.8Å		\|PDB= 9hvp \|SIZE=350\|CAPTION= <scene name='initialview01'>9hvp</scene>, resolution 2.8Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=PHQ:FORMIC ACID BENZYL ESTER'>PHQ</scene>	+	\|LIGAND= <scene name='pdbligand=COR:2,4-DIAMINO-1,5-DIPHENYL-3-HYDROXYPENTANE'>COR</scene>, <scene name='pdbligand=PHQ:FORMIC+ACID+BENZYL+ESTER'>PHQ</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9hvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9hvp OCA], [http://www.ebi.ac.uk/pdbsum/9hvp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=9hvp RCSB]</span>
	}}		}}

Line 24:		Line 27:
	[[Category: Erickson, J.]]		[[Category: Erickson, J.]]
	[[Category: Neidhart, D J.]]		[[Category: Neidhart, D J.]]
-	[[Category: PHQ]]
	[[Category: hydrolase(acid proteinase)]]		[[Category: hydrolase(acid proteinase)]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:16:17 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:46:07 2008''

OCA at 17:16, 20 March 2008

OCA — Thu, 20 Mar 2008 17:16:20 GMT

←Older revision		Revision as of 17:16, 20 March 2008
Line 1:		Line 1:
-	[[Image:9hvp.gif\|left\|200px]]~~<br /><applet load~~="9hvp~~" size~~="350~~" color~~=~~"white" frame="true" align="right" spinBox="true"~~	+	[[Image:9hvp.gif\|left\|200px]]
-	~~caption~~="9hvp, resolution 2.8Å" />	+
-	'''DESIGN, ACTIVITY AND 2.8 ANGSTROMS CRYSTAL STRUCTURE OF A C2 SYMMETRIC INHIBITOR COMPLEXED TO HIV-1 PROTEASE'''~~<br />~~	+	{{Structure
		+	\|PDB= 9hvp \|SIZE=350\|CAPTION= <scene name='initialview01'>9hvp</scene>, resolution 2.8Å
		+	\|SITE=
		+	\|LIGAND= <scene name='pdbligand=PHQ:FORMIC ACID BENZYL ESTER'>PHQ</scene>
		+	\|ACTIVITY=
		+	\|GENE=
		+	}}
		+
		+	'''DESIGN, ACTIVITY AND 2.8 ANGSTROMS CRYSTAL STRUCTURE OF A C2 SYMMETRIC INHIBITOR COMPLEXED TO HIV-1 PROTEASE'''
		+

	==Overview==		==Overview==
Line 7:		Line 16:

	==About this Structure==		==About this Structure==
-	9HVP is a [~~http://en.wikipedia.org/wiki/Single_protein~~ Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1~~] with <scene name='pdbligand=PHQ:'>PHQ</scene> as [http://en.wikipedia.org/wiki/ligand ligand~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA].	+	9HVP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9HVP OCA].

	==Reference==		==Reference==
-	Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease., Erickson J, Neidhart DJ, VanDrie J, Kempf DJ, Wang XC, Norbeck DW, Plattner JJ, Rittenhouse JW, Turon M, Wideburg N, et al., Science. 1990 Aug 3;249(4968):527-33. PMID:[http://~~ispc~~.~~weizmann~~.ac.~~il/~~/~~pmbin~~/~~getpm?pmid=~~2200122 2200122]	+	Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease., Erickson J, Neidhart DJ, VanDrie J, Kempf DJ, Wang XC, Norbeck DW, Plattner JJ, Rittenhouse JW, Turon M, Wideburg N, et al., Science. 1990 Aug 3;249(4968):527-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2200122 2200122]
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Single protein]]		[[Category: Single protein]]
Line 18:		Line 27:
	[[Category: hydrolase(acid proteinase)]]		[[Category: hydrolase(acid proteinase)]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Feb 21~~ 19:18:34 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:16:17 2008''