3ou4 - Revision history

OCA at 10:36, 21 February 2024

2024-02-21T10:36:30Z

←Older revision		Revision as of 10:36, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3ou4' size='340' side='right'caption='[[3ou4]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3ou4' size='340' side='right'caption='[[3ou4]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ou4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ou4]] is a 3 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=3OU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OU4 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[3ots\|3ots]], [[3oty\|3oty]], [[3ou1\|3ou1]], [[3ou3\|3ou3]], [[3oua\|3oua]], [[3oub\|3oub]], [[3ouc\|3ouc]], [[3oud\|3oud]]</div></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]] 1.6Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">pol ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=11676 9HIV1])~~</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=3ou4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ou4 OCA], [https://pdbe.org/3ou4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ou4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ou4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ou4 ProSAT]</span></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=3ou4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ou4 OCA], [https://pdbe.org/3ou4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ou4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ou4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ou4 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/POL_HV1Y2 POL_HV1Y2] 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).
-	~~Under drug selection pressure~~, ~~emerging mutations render HIV~~-~~1 protease drug resistant~~, ~~leading~~ to the ~~therapy failure~~ in ~~anti~~-~~HIV treatment~~. It ~~is known that nine substrate cleavage site peptides bind~~ to ~~wild type~~ (WT) ~~HIV~~-~~1 protease~~ in ~~a conserved pattern~~. ~~However~~, ~~how~~ the ~~multidrug~~-~~resistant (MDR)~~ HIV-1 ~~protease binds~~ to the ~~substrate cleavage site peptides~~ is ~~yet~~ to ~~be determined~~. ~~MDR769 HIV-1~~ protease ~~(resistant mutations at residues 10~~, 36, 46, ~~54, 62, 63, 71, 82, 84~~, and 90) ~~was selected for present study to understand~~ the ~~binding~~ to ~~its natural substrates~~. ~~MDR769 HIV~~-~~1 protease was co~~-~~crystallized with nine substrate cleavage~~ site ~~hepta~~-~~peptides~~. ~~Crystallographic studies show that MDR769 HIV~~-~~1 protease has an expanded substrate envelope with wide open flaps~~. ~~Furthermore~~, ~~ligand binding energy calculations indicate weaker binding~~ in ~~MDR769 HIV~~-~~1 protease~~-~~substrate complexes~~. ~~These results help in designing~~ the ~~next generation~~ of ~~HIV~~-~~1 protease inhibitors~~ by ~~targeting~~ the ~~MDR HIV~~-~~1 protease~~.	+
-		+
-	~~Nine Crystal Structures Determine~~ the ~~Substrate Envelope~~ of the ~~MDR HIV~~-~~1 Protease~~.,~~Liu Z~~, ~~Wang~~ Y, ~~Brunzelle J~~, ~~Kovari IA~~, ~~Kovari LC Protein J~~. ~~2011 Mar 12~~. ~~PMID:21394574<ref>PMID:21394574</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®~~, a ~~database~~ of the U.~~S. National Library~~ of ~~Medicine~~.~~<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3ou4" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Immunodeficiency virus protease 3D structures\|Immunodeficiency virus protease 3D structures]]		*[[Immunodeficiency virus protease 3D structures\|Immunodeficiency virus protease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brunzelle, J]]	+	[[Category: Brunzelle J]]
-	[[Category: Kovari~~, I A~~]]	+	[[Category: Kovari IA]]
-	[[Category: Kovari~~, L C~~]]	+	[[Category: Kovari LC]]
-	[[Category: Liu, Z]]	+	[[Category: Liu Z]]
-	[[Category: Wang, Y]]	+	[[Category: Wang Y]]
-	~~[[Category: Hiv-1 protease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-peptide complex]]~~	+
-	~~[[Category: None]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Tf/pr substrate peptide]]~~	+
-	~~[[Category: This sequence occurs naturally in humans~~]]	+

OCA at 10:57, 18 May 2022

2022-05-18T10:57:29Z

←Older revision		Revision as of 10:57, 18 May 2022
Line 1:		Line 1:

	==MDR769 HIV-1 protease complexed with TF/PR hepta-peptide==		==MDR769 HIV-1 protease complexed with TF/PR hepta-peptide==
-	<StructureSection load='3ou4' size='340' side='right' caption='[[3ou4]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3ou4' size='340' side='right'caption='[[3ou4]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ou4]] is a 3 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=3OU4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3OU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ou4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OU4 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ots\|3ots]], [[3oty\|3oty]], [[3ou1\|3ou1]], [[3ou3\|3ou3]], [[3oua\|3oua]], [[3oub\|3oub]], [[3ouc\|3ouc]], [[3oud\|3oud]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ots\|3ots]], [[3oty\|3oty]], [[3ou1\|3ou1]], [[3ou3\|3ou3]], [[3oua\|3oua]], [[3oub\|3oub]], [[3ouc\|3ouc]], [[3oud\|3oud]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=3ou4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ou4 OCA], [~~http~~://pdbe.org/3ou4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ou4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ou4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ou4 ProSAT]</span></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=3ou4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ou4 OCA], [https://pdbe.org/3ou4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ou4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ou4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ou4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[~~Virus~~ protease\|~~Virus~~ protease]]	+	*[[Immunodeficiency virus protease 3D structures\|Immunodeficiency virus protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Brunzelle, J]]		[[Category: Brunzelle, J]]
	[[Category: Kovari, I A]]		[[Category: Kovari, I A]]

OCA at 03:50, 10 December 2016

2016-12-10T03:50:09Z

←Older revision		Revision as of 03:50, 10 December 2016
Line 1:		Line 1:
		+
	==MDR769 HIV-1 protease complexed with TF/PR hepta-peptide==		==MDR769 HIV-1 protease complexed with TF/PR hepta-peptide==
	<StructureSection load='3ou4' size='340' side='right' caption='[[3ou4]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3ou4' size='340' side='right' caption='[[3ou4]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ou4]] is a 3 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=3OU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ou4]] is a 3 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=3OU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OU4 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ots\|3ots]], [[3oty\|3oty]], [[3ou1\|3ou1]], [[3ou3\|3ou3]], [[3oua\|3oua]], [[3oub\|3oub]], [[3ouc\|3ouc]], [[3oud\|3oud]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ots\|3ots]], [[3oty\|3oty]], [[3ou1\|3ou1]], [[3ou3\|3ou3]], [[3oua\|3oua]], [[3oub\|3oub]], [[3ouc\|3ouc]], [[3oud\|3oud]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 ~~Human immunodeficiency virus 1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=3ou4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ou4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ou4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ou4 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=3ou4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ou4 OCA], [http://pdbe.org/3ou4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ou4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ou4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ou4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3ou4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human immunodeficiency virus 1]]
	[[Category: Brunzelle, J]]		[[Category: Brunzelle, J]]
	[[Category: Kovari, I A]]		[[Category: Kovari, I A]]

OCA at 11:34, 9 December 2014

2014-12-09T11:34:17Z

←Older revision		Revision as of 11:34, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3ou4.~~png~~\|~~left~~\|~~200px~~]]	+	==MDR769 HIV-1 protease complexed with TF/PR hepta-peptide==
		+	<StructureSection load='3ou4' size='340' side='right' caption='[[3ou4]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ou4]] is a 3 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=3OU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OU4 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ots\|3ots]], [[3oty\|3oty]], [[3ou1\|3ou1]], [[3ou3\|3ou3]], [[3oua\|3oua]], [[3oub\|3oub]], [[3ouc\|3ouc]], [[3oud\|3oud]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 Human immunodeficiency virus 1])</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=3ou4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ou4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ou4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ou4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Under drug selection pressure, emerging mutations render HIV-1 protease drug resistant, leading to the therapy failure in anti-HIV treatment. It is known that nine substrate cleavage site peptides bind to wild type (WT) HIV-1 protease in a conserved pattern. However, how the multidrug-resistant (MDR) HIV-1 protease binds to the substrate cleavage site peptides is yet to be determined. MDR769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, and 90) was selected for present study to understand the binding to its natural substrates. MDR769 HIV-1 protease was co-crystallized with nine substrate cleavage site hepta-peptides. Crystallographic studies show that MDR769 HIV-1 protease has an expanded substrate envelope with wide open flaps. Furthermore, ligand binding energy calculations indicate weaker binding in MDR769 HIV-1 protease-substrate complexes. These results help in designing the next generation of HIV-1 protease inhibitors by targeting the MDR HIV-1 protease.

-	~~{{STRUCTURE_3ou4\| PDB=3ou4 \| SCENE= }}~~	+	Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease.,Liu Z, Wang Y, Brunzelle J, Kovari IA, Kovari LC Protein J. 2011 Mar 12. PMID:21394574<ref>PMID:21394574</ref>

-	~~===MDR769 HIV-1 protease complexed with TF~~/~~PR hepta-peptide===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21394574}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ou4]] is~~ a ~~3 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=3OU4 OCA].~~	+

	==See Also==		==See Also==
	*[[Virus protease\|Virus protease]]		*[[Virus protease\|Virus protease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021394574<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
-	[[Category: Brunzelle, J.]]	+	[[Category: Brunzelle, J]]
-	[[Category: Kovari, I A.]]	+	[[Category: Kovari, I A]]
-	[[Category: Kovari, L C.]]	+	[[Category: Kovari, L C]]
-	[[Category: Liu, Z.]]	+	[[Category: Liu, Z]]
-	[[Category: Wang, Y.]]	+	[[Category: Wang, Y]]
	[[Category: Hiv-1 protease]]		[[Category: Hiv-1 protease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
Line 27:		Line 34:
	[[Category: Protease]]		[[Category: Protease]]
	[[Category: Tf/pr substrate peptide]]		[[Category: Tf/pr substrate peptide]]
-	[[Category: This sequence occurs naturally in humans.]]	+	[[Category: This sequence occurs naturally in humans]]

OCA at 20:58, 20 October 2012

2012-10-20T20:58:42Z

←Older revision		Revision as of 20:58, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3ou4]] is a 3 chain structure ~~of [[Virus protease]]~~ 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=3OU4 OCA].	+	[[3ou4]] is a 3 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=3OU4 OCA].

	==See Also==		==See Also==

OCA at 12:12, 27 July 2012

2012-07-27T12:12:42Z

←Older revision		Revision as of 12:12, 27 July 2012
Line 1:		Line 1:
	[[Image:3ou4.png\|left\|200px]]		[[Image:3ou4.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ou4", 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_3ou4\| PDB=3ou4 \| SCENE= }}		{{STRUCTURE_3ou4\| PDB=3ou4 \| SCENE= }}

	===MDR769 HIV-1 protease complexed with TF/PR hepta-peptide===		===MDR769 HIV-1 protease complexed with TF/PR hepta-peptide===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21394574}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21394574 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21394574}}		{{ABSTRACT_PUBMED_21394574}}

	==About this Structure==		==About this Structure==
-	[[3ou4]] is a 3 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=3OU4 OCA].	+	[[3ou4]] is a 3 chain structure of [[Virus protease]] 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=3OU4 OCA].
		+
		+	==See Also==
		+	*[[Virus protease\|Virus protease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21394574~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021394574</ref><references group="xtra"/>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Brunzelle, J.]]		[[Category: Brunzelle, J.]]
Line 29:		Line 21:
	[[Category: Liu, Z.]]		[[Category: Liu, Z.]]
	[[Category: Wang, Y.]]		[[Category: Wang, Y.]]
		+	[[Category: Hiv-1 protease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-peptide complex]]
		+	[[Category: None]]
		+	[[Category: Protease]]
		+	[[Category: Tf/pr substrate peptide]]
		+	[[Category: This sequence occurs naturally in humans.]]

OCA at 09:48, 21 April 2011

2011-04-21T09:48:09Z

←Older revision		Revision as of 09:48, 21 April 2011
Line 1:		Line 1:
-	[[Image:3ou4.~~jpg~~\|left\|200px]]	+	[[Image:3ou4.png\|left\|200px]]

	<!--		<!--

OCA at 08:03, 30 March 2011

2011-03-30T08:03:56Z

←Older revision		Revision as of 08:03, 30 March 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3ou4.jpg\|left\|200px]]

-	The ~~entry 3ou4~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ou4", 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_3ou4\| PDB=3ou4 \| SCENE= }}

-	~~Authors: Liu, Z., Wang, Y., Brunzelle, J., Kovari, I.A., Kovari, L.C.~~	+	===MDR769 HIV-1 protease complexed with TF/PR hepta-peptide===

-	~~Description~~: ~~MDR769 HIV~~-~~1 protease complexed~~ with TF/~~PR hepta~~-~~peptide~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21394574}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21394574 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21394574}}
		+
		+	==About this Structure==
		+	[[3ou4]] is a 3 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=3OU4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21394574</ref><references group="xtra"/>
		+	[[Category: Human immunodeficiency virus 1]]
		+	[[Category: Brunzelle, J.]]
		+	[[Category: Kovari, I A.]]
		+	[[Category: Kovari, L C.]]
		+	[[Category: Liu, Z.]]
		+	[[Category: Wang, Y.]]

OCA: Protected "3ou4" [edit=sysop:move=sysop]

2010-12-29T18:12:13Z

Protected "3ou4" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:12, 29 December 2010

OCA at 18:12, 29 December 2010

2010-12-29T18:12:12Z

←Older revision		Revision as of 18:12, 29 December 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3ou4 is ON HOLD	+	The entry 3ou4 is ON HOLD until Paper Publication

	Authors: Liu, Z., Wang, Y., Brunzelle, J., Kovari, I.A., Kovari, L.C.		Authors: Liu, Z., Wang, Y., Brunzelle, J., Kovari, I.A., Kovari, L.C.

	Description: MDR769 HIV-1 protease complexed with TF/PR hepta-peptide		Description: MDR769 HIV-1 protease complexed with TF/PR hepta-peptide
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 14:35:00 2010''