4ka2: Difference between revisions

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-{{STRUCTURE_4ka2|  PDB=4ka2  |  SCENE=  }}
+==Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120==
-===Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120===
+<StructureSection load='4ka2' size='340' side='right' caption='[[4ka2]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
-{{ABSTRACT_PUBMED_23710622}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ka2]] 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=4KA2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KA2 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=MPT:BETA-MERCAPTOPROPIONIC+ACID'>MPT</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=U3X:4-[(CYCLOHEXYLMETHYL)AMINO]-L-PHENYLALANINE'>U3X</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jzw|4jzw]], [[4jzz|4jzz]], [[4k0a|4k0a]], [[2i5y|2i5y]], [[2i60|2i60]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gp120 ([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=4ka2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ka2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ka2 RCSB], [http://www.ebi.ac.uk/pdbsum/4ka2 PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ligand affinities can be optimized by interfacial cavity filling. A hollow (Phe43 cavity) between HIV-1 surface glycoprotein (gp120) and cluster of differentiation 4 (CD4) receptor extends beyond residue phenylalanine 43 of CD4 and cannot be fully accessed by natural amino acids. To increase HIV-1 gp120 affinity for a family of CD4-mimetic miniproteins (miniCD4s), we targeted the gp120 Phe43 cavity with 11 non-natural phenylalanine derivatives, introduced into a miniCD4 named M48 (1). The best derivative, named M48U12 (13), bound HIV-1 YU2 gp120 with 8 pM affinity and showed potent HIV-1 neutralization. It contained a methylcyclohexyl derivative of 4-aminophenylalanine, and its cocrystal structure with gp120 revealed the cyclohexane ring buried within the gp120 hydrophobic core but able to assume multiple orientations in the binding pocket, and the aniline nitrogen potentially providing a focus for further improvement. Altogether, the results provide a framework for filling the interfacial Phe43 cavity to enhance miniCD4 affinity.
-==About this Structure==
+Interfacial Cavity Filling To Optimize CD4-Mimetic Miniprotein Interactions with HIV-1 Surface Glycoprotein.,Morellato-Castillo L, Acharya P, Combes O, Michiels J, Descours A, Ramos OH, Yang Y, Vanham G, Arien KK, Kwong PD, Martin L, Kessler P J Med Chem. 2013 Jun 11. PMID:23710622<ref>PMID:23710622</ref>
-[[4ka2]] 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=4KA2 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:023710622</ref><references group="xtra"/><references/>
+</div>
+==See Also==
+*[[Gp120|Gp120]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Human immunodeficiency virus 1]]
-[[Category: Acharya, P.]]
+[[Category: Acharya, P]]
-[[Category: Kwong, P D.]]
+[[Category: Kwong, P D]]
 [[Category: Cd4 mimic]]
 [[Category: Gp120]]