3nxn - Revision history

OCA at 10:01, 14 February 2024

OCA — Wed, 14 Feb 2024 10:01:59 GMT

←Older revision		Revision as of 10:01, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='3nxn' size='340' side='right'caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3nxn' size='340' side='right'caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nxn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/HIV-1_M:B_ARV2/SF2 HIV-1 M:B_ARV2/SF2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NXN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KVS:N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-ACETYL-L-THREONYL)AMINO]-3-METHYLPENT-4-ENOYL}AMINO)-2-BUTYL-4,4-DIHYDROXYNONANOYL]-L-GLUTAMINYL-L-ARGININAMIDE'>KVS~~</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA~~</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=OIL:(2S,3S)-2-HYDROXY-3-METHYLPENTANOIC+ACID'>OIL</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=KVS:N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-ACETYL-L-THREONYL)AMINO]-3-METHYLPENT-4-ENOYL}AMINO)-2-BUTYL-4,4-DIHYDROXYNONANOYL]-L-GLUTAMINYL-L-ARGININAMIDE'>KVS</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=OIL:(2S,3S)-2-HYDROXY-3-METHYLPENTANOIC+ACID'>OIL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3nwx\|3nwx]], [[3nwq\|3nwq]], [[3nxe\|3nxe]], [[3hau\|3hau]], [[3hdk\|3hdk]], [[3hlo\|3hlo]], [[3nyg\|3nyg]]</div></td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] </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=3nxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nxn OCA], [https://pdbe.org/3nxn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nxn RCSB], [https://www.ebi.ac.uk/pdbsum/3nxn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nxn 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=3nxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nxn OCA], [https://pdbe.org/3nxn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nxn RCSB], [https://www.ebi.ac.uk/pdbsum/3nxn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nxn ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/POL_HV1A2 POL_HV1A2] 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).
-	~~We have used chemical~~ protein ~~synthesis~~ and ~~advanced physical methods to probe dynamics~~-~~function correlations for~~ the ~~HIV~~-~~1 protease~~, ~~an enzyme~~ that ~~has received considerable attention as a target for the treatment of AIDS~~. ~~Chemical synthesis was used~~ to ~~prepare~~ a ~~series~~ of ~~unique analogues~~ of the ~~HIV~~-~~1 protease~~ in which the ~~flexibility~~ of the ~~"flap" structures~~ (~~residues 37~~-61 in ~~each monomer~~ of the ~~homodimeric~~ protein ~~molecule~~) ~~was systematically varied~~. ~~These analogue enzymes were further studied by X~~-~~ray crystallography~~, ~~NMR relaxation, and pulse~~-~~EPR methods~~, ~~in conjunction~~ with ~~molecular dynamics simulations~~. ~~We show~~ that ~~conformational isomerization~~ in the ~~flaps is correlated with structural reorganization~~ of ~~residues~~ in the ~~active~~ site, and ~~that it~~ is ~~preorganization~~ of the ~~active site that~~ is a ~~rate~~-~~limiting factor in catalysis~~.	+
-		+
-	~~Protein conformational dynamics in~~ the ~~mechanism~~ of ~~HIV~~-~~1 protease catalysis~~.,~~Torbeev VY, Raghuraman~~ H, ~~Hamelberg D~~, ~~Tonelli M~~, ~~Westler WM, Perozo E~~, ~~Kent SB Proc Natl Acad Sci U S A~~. ~~2011 Dec 27;108~~(52)~~:20982-7~~. ~~Epub 2011 Dec 8~~. ~~PMID:22158985<ref>PMID:22158985</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®~~, a ~~database~~ of the U.S. ~~National Library~~ of ~~Medicine~~.~~<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe~~-~~citations 3nxn" 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: HIV-1 ~~retropepsin~~]]	+	[[Category: HIV-1 M:B_ARV2/SF2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kent~~, S B.H~~]]	+	[[Category: Kent SBH]]
-	[[Category: Torbeev~~, V Y]]~~	+	[[Category: Torbeev VY]]
-	~~[[Category: Beta-barrel]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 07:11, 12 May 2022

OCA — Thu, 12 May 2022 07:11:35 GMT

←Older revision		Revision as of 07:11, 12 May 2022
Line 3:		Line 3:
	<StructureSection load='3nxn' size='340' side='right'caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3nxn' size='340' side='right'caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3NXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NXN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KVS:N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-ACETYL-L-THREONYL)AMINO]-3-METHYLPENT-4-ENOYL}AMINO)-2-BUTYL-4,4-DIHYDROXYNONANOYL]-L-GLUTAMINYL-L-ARGININAMIDE'>KVS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KVS:N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-ACETYL-L-THREONYL)AMINO]-3-METHYLPENT-4-ENOYL}AMINO)-2-BUTYL-4,4-DIHYDROXYNONANOYL]-L-GLUTAMINYL-L-ARGININAMIDE'>KVS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=OIL:(2S,3S)-2-HYDROXY-3-METHYLPENTANOIC+ACID'>OIL</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=OIL:(2S,3S)-2-HYDROXY-3-METHYLPENTANOIC+ACID'>OIL</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nwx\|3nwx]], [[3nwq\|3nwq]], [[3nxe\|3nxe]], [[3hau\|3hau]], [[3hdk\|3hdk]], [[3hlo\|3hlo]], [[3nyg\|3nyg]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3nwx\|3nwx]], [[3nwq\|3nwq]], [[3nxe\|3nxe]], [[3hau\|3hau]], [[3hdk\|3hdk]], [[3hlo\|3hlo]], [[3nyg\|3nyg]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] </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=3nxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nxn OCA], [~~http~~://pdbe.org/3nxn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3nxn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3nxn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3nxn 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=3nxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nxn OCA], [https://pdbe.org/3nxn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nxn RCSB], [https://www.ebi.ac.uk/pdbsum/3nxn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nxn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:35, 31 July 2019

OCA — Wed, 31 Jul 2019 06:35:53 GMT

←Older revision		Revision as of 06:35, 31 July 2019
Line 1:		Line 1:

	==X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor==		==X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor==
-	<StructureSection load='3nxn' size='340' side='right' caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3nxn' size='340' side='right'caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NXN FirstGlance]. <br>		<table><tr><td colspan='2'>[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NXN FirstGlance]. <br>
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Immunodeficiency virus protease\|Immunodeficiency virus protease]]	+	*[[Immunodeficiency virus protease 3D structures\|Immunodeficiency virus protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: HIV-1 retropepsin]]		[[Category: HIV-1 retropepsin]]
		+	[[Category: Large Structures]]
	[[Category: Kent, S B.H]]		[[Category: Kent, S B.H]]
	[[Category: Torbeev, V Y]]		[[Category: Torbeev, V Y]]
	[[Category: Beta-barrel]]		[[Category: Beta-barrel]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 10:18, 30 January 2019

OCA — Wed, 30 Jan 2019 10:18:43 GMT

←Older revision		Revision as of 10:18, 30 January 2019
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[~~Virus~~ protease\|~~Virus~~ protease]]	+	*[[Immunodeficiency virus protease\|Immunodeficiency virus protease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:01, 10 December 2016

OCA — Sat, 10 Dec 2016 04:01:59 GMT

←Older revision		Revision as of 04:01, 10 December 2016
Line 1:		Line 1:
		+
	==X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor==		==X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor==
	<StructureSection load='3nxn' size='340' side='right' caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3nxn' size='340' side='right' caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nwx\|3nwx]], [[3nwq\|3nwq]], [[3nxe\|3nxe]], [[3hau\|3hau]], [[3hdk\|3hdk]], [[3hlo\|3hlo]], [[3nyg\|3nyg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nwx\|3nwx]], [[3nwq\|3nwq]], [[3nxe\|3nxe]], [[3hau\|3hau]], [[3hdk\|3hdk]], [[3hlo\|3hlo]], [[3nyg\|3nyg]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] </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=3nxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nxn RCSB], [http://www.ebi.ac.uk/pdbsum/3nxn 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=3nxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nxn OCA], [http://pdbe.org/3nxn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nxn RCSB], [http://www.ebi.ac.uk/pdbsum/3nxn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nxn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 3nxn" style="background-color:#fffaf0;"></div>

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

OCA at 11:59, 9 December 2014

OCA — Tue, 09 Dec 2014 11:59:17 GMT

←Older revision		Revision as of 11:59, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3nxn.~~png~~\|~~left~~\|~~200px~~]]	+	==X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor==
		+	<StructureSection load='3nxn' size='340' side='right' caption='[[3nxn]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NXN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KVS:N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-ACETYL-L-THREONYL)AMINO]-3-METHYLPENT-4-ENOYL}AMINO)-2-BUTYL-4,4-DIHYDROXYNONANOYL]-L-GLUTAMINYL-L-ARGININAMIDE'>KVS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=OIL:(2S,3S)-2-HYDROXY-3-METHYLPENTANOIC+ACID'>OIL</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nwx\|3nwx]], [[3nwq\|3nwq]], [[3nxe\|3nxe]], [[3hau\|3hau]], [[3hdk\|3hdk]], [[3hlo\|3hlo]], [[3nyg\|3nyg]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] </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=3nxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nxn RCSB], [http://www.ebi.ac.uk/pdbsum/3nxn PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was used to prepare a series of unique analogues of the HIV-1 protease in which the flexibility of the "flap" structures (residues 37-61 in each monomer of the homodimeric protein molecule) was systematically varied. These analogue enzymes were further studied by X-ray crystallography, NMR relaxation, and pulse-EPR methods, in conjunction with molecular dynamics simulations. We show that conformational isomerization in the flaps is correlated with structural reorganization of residues in the active site, and that it is preorganization of the active site that is a rate-limiting factor in catalysis.

-	~~{{STRUCTURE_3nxn\| PDB=3nxn \| SCENE= }}~~	+	Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.,Torbeev VY, Raghuraman H, Hamelberg D, Tonelli M, Westler WM, Perozo E, Kent SB Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):20982-7. Epub 2011 Dec 8. PMID:22158985<ref>PMID:22158985</ref>

-	~~===X-ray structure of ester chemical analogue 'covalent dimer' [Ile50~~,~~O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22158985}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3nxn]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3NXN OCA].~~	+

	==See Also==		==See Also==
	*[[Virus protease\|Virus protease]]		*[[Virus protease\|Virus protease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:022158985<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: HIV-1 retropepsin]]		[[Category: HIV-1 retropepsin]]
-	[[Category: Kent, S B.H.]]	+	[[Category: Kent, S B.H]]
-	[[Category: Torbeev, V Y.]]	+	[[Category: Torbeev, V Y]]
	[[Category: Beta-barrel]]		[[Category: Beta-barrel]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 06:00, 20 October 2012

OCA — Sat, 20 Oct 2012 06:00:23 GMT

←Older revision		Revision as of 06:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3nxn]] is a 1 chain structure ~~of [[Virus protease]]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA].	+	[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA].

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

OCA at 11:48, 25 July 2012

OCA — Wed, 25 Jul 2012 11:48:21 GMT

←Older revision		Revision as of 11:48, 25 July 2012
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	[[Image:3nxn.png\|left\|200px]]		[[Image:3nxn.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3nxn", 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_3nxn\| PDB=3nxn \| SCENE= }}		{{STRUCTURE_3nxn\| PDB=3nxn \| SCENE= }}

	===X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor===		===X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22158985}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22158985 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22158985}}		{{ABSTRACT_PUBMED_22158985}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Virus protease]]	+	*[[Virus protease\|Virus protease]]

	==Reference==		==Reference==

OCA at 05:32, 11 January 2012

OCA — Wed, 11 Jan 2012 05:32:56 GMT

←Older revision		Revision as of 05:32, 11 January 2012
Line 1:		Line 1:
-	[[Image:3nxn.~~jpg~~\|left\|200px]]	+	[[Image:3nxn.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor===		===X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22158985}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22158985 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22158985}}

	==About this Structure==		==About this Structure==
-	[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA].	+	[[3nxn]] is a 1 chain structure of [[Virus protease]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA].
		+
		+	==See Also==
		+	*[[Virus protease]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022158985</ref><references group="xtra"/>
	[[Category: HIV-1 retropepsin]]		[[Category: HIV-1 retropepsin]]
	[[Category: Kent, S B.H.]]		[[Category: Kent, S B.H.]]

OCA at 08:31, 2 November 2011

OCA — Wed, 02 Nov 2011 08:31:54 GMT

←Older revision		Revision as of 08:31, 2 November 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3nxn.jpg\|left\|200px]]

-	The ~~entry 3nxn~~ is ~~ON HOLD~~ ~~until Jan 10 2013~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3nxn", 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_3nxn\| PDB=3nxn \| SCENE= }}

-	~~Authors: Torbeev~~, ~~V.Y., Kent, S.B.H.~~	+	===X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor===

-	~~Description: X-ray~~ structure ~~of ester chemical analogue 'covalent dimer'~~ [~~Ile50,O~~-~~Ile50'~~]HIV-1 ~~protease complexed with KVS~~-1 inhibitor	+
		+	==About this Structure==
		+	[[3nxn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NXN OCA].
		+	[[Category: HIV-1 retropepsin]]
		+	[[Category: Kent, S B.H.]]
		+	[[Category: Torbeev, V Y.]]
		+	[[Category: Beta-barrel]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]