5kr2: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:


==Protease PR5-SQV==
==Protease PR5-SQV==
<StructureSection load='5kr2' size='340' side='right' caption='[[5kr2]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
<StructureSection load='5kr2' size='340' side='right'caption='[[5kr2]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5kr2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KR2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5kr2]] is a 4 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=5KR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KR2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROC:(2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT-BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3-HYDROXY-1-PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE'>ROC</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]] 1.78&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kqx|5kqx]], [[5kqy|5kqy]], [[5kqz|5kqz]], [[5kr0|5kr0]], [[5kr1|5kr1]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ROC:(2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT-BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3-HYDROXY-1-PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE'>ROC</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=5kr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kr2 OCA], [http://pdbe.org/5kr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kr2 RCSB], [http://www.ebi.ac.uk/pdbsum/5kr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kr2 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=5kr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kr2 OCA], [https://pdbe.org/5kr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kr2 RCSB], [https://www.ebi.ac.uk/pdbsum/5kr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kr2 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/V5YAB1_9HIV1 V5YAB1_9HIV1]
Multidrug resistance to current FDA approved HIV-1 protease (PR) inhibitors drives the need to understand the fundamental mechanisms of how drug-pressure selected mutations, which are oftentimes natural polymorphisms, elicit their effect on enzyme function and resistance. Here, the impact of hinge-region natural polymorphism at residue 35 - glutamate to aspartate (E35D) - alone and in conjunction with residue 57 arginine to lysine (R57K) are characterized with the goal of understanding how altered salt-bridge interactions between the hinge and flap regions are associated with changes in structure, motional dynamics, conformational sampling, kinetic parameters, and inhibitor affinity. The combined results reveal that the single E35D substitution leads to diminished salt-bridge interactions between residue 35 and 57 and gives rise to the stabilization of open-like conformational states with overall increased backbone dynamics. In HIV-1 PR constructs where sites 35 and 57 are both mutated (e.g. E35D, R57K), X-ray structures reveal an altered network of interactions that replace the salt-bridge thus stabilizing the structural integrity between the flap and hinge regions. In spite of the altered conformational sampling and dynamics when the salt bridge is disrupted, enzyme kinetic parameters and inhibition constants are similar to those obtained for subtype B PR. Results demonstrate that these hinge region natural polymorphisms, which may arise as drug pressure secondary mutations, alter protein dynamics and conformational landscape, which are important thermodynamic parameters to consider for development of inhibitors that target for non-subtype B PR.


Effects of Hinge Region Natural Polymorphisms on Human Immunodeficiency Virus-1 Protease Structure, Dynamics and Drug-Pressure Evolution.,Liu Z, Huang X, Hu L, Pham L, Poole KM, Tang Y, Mahon BP, Tang W, Li K, Goldfarb NE, Dunn BM, McKenna R, Fanucci GE J Biol Chem. 2016 Aug 30. pii: jbc.M116.747568. PMID:27576689<ref>PMID:27576689</ref>
==See Also==
 
*[[Immunodeficiency virus protease 3D structures|Immunodeficiency virus protease 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5kr2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Fanucci, G E]]
[[Category: Human immunodeficiency virus 1]]
[[Category: Liu, Z]]
[[Category: Large Structures]]
[[Category: Mahon, B P]]
[[Category: Fanucci GE]]
[[Category: McKenna, R]]
[[Category: Liu Z]]
[[Category: Poole, K M]]
[[Category: Mahon BP]]
[[Category: E35d]]
[[Category: McKenna R]]
[[Category: Hiv-1 protease]]
[[Category: Poole KM]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Natural polymorphism]]
[[Category: Salt-bridge interaction]]

Latest revision as of 15:41, 6 March 2024

Protease PR5-SQVProtease PR5-SQV

Structural highlights

5kr2 is a 4 chain structure with sequence from Human immunodeficiency virus 1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.78Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

V5YAB1_9HIV1

See Also

5kr2, resolution 1.78Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=5kr2&oldid=4081058"