3kq0: Difference between revisions

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-{{STRUCTURE_3kq0|  PDB=3kq0  |  SCENE=  }}
-===Crystal structure of human alpha1-acid glycoprotein===
-{{ABSTRACT_PUBMED_18823996}}
-==Function==
+==Crystal structure of human alpha1-acid glycoprotein==
+<StructureSection load='3kq0' size='340' side='right'caption='[[3kq0]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3kq0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3bx6 3bx6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KQ0 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=JIM:(2R)-2,3-DIHYDROXYPROPYL+ACETATE'>JIM</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bx6|3bx6]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGP-A, AGP1, ORM, ORM1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3kq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kq0 OCA], [http://pdbe.org/3kq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kq0 RCSB], [http://www.ebi.ac.uk/pdbsum/3kq0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kq0 ProSAT]</span></td></tr>
+</table>
+== Function ==
 [[http://www.uniprot.org/uniprot/A1AG1_HUMAN A1AG1_HUMAN]] Functions as transport protein in the blood stream. Binds various ligands in the interior of its beta-barrel domain. Also binds synthetic drugs and influences their distribution and availability in the body. Appears to function in modulating the activity of the immune system during the acute-phase reaction.<ref>PMID:17008009</ref> <ref>PMID:17321687</ref>
+== 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/kq/3kq0_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/main_output.php?pdb_ID=3kq0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Alpha(1)-acid glycoprotein (AGP) is an important drug-binding protein in human plasma and, as an acute-phase protein, it has a strong influence on pharmacokinetics and pharmacodynamics of many pharmaceuticals. We report the crystal structure of the recombinant unglycosylated human AGP at 1.8 A resolution, which was solved using the new method of UV-radiation-damage-induced phasing (UV RIP). AGP reveals a typical lipocalin fold comprising an eight-stranded beta-barrel. Of the four loops that form the entrance to the ligand-binding site, loop 1, which connects beta-strands A and B, is among the longest observed so far and exhibits two full turns of an alpha-helix. Furthermore, it carries one of the five N-linked glycosylation sites, while a second one occurs underneath the tip of loop 2. The branched, partly hydrophobic, and partly acidic cavity, together with the presumably flexible loop 1 and the two sugar side chains at its entrance, explains the diverse ligand spectrum of AGP, which is known to vary with changes in glycosylation pattern.
-==About this Structure==
+The 1.8-A crystal structure of alpha1-acid glycoprotein (Orosomucoid) solved by UV RIP reveals the broad drug-binding activity of this human plasma lipocalin.,Schonfeld DL, Ravelli RB, Mueller U, Skerra A J Mol Biol. 2008 Dec 12;384(2):393-405. Epub 2008 Sep 16. PMID:18823996<ref>PMID:18823996</ref>
-[[3kq0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3bx6 3bx6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KQ0 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:018823996</ref><references group="xtra"/><references/>
+</div>
-[[Category: Homo sapiens]]
+<div class="pdbe-citations 3kq0" style="background-color:#fffaf0;"></div>
-[[Category: Mueller, U.]]
+== References ==
-[[Category: Ravelli, R B.G.]]
+<references/>
-[[Category: Schiefner, A.]]
+__TOC__
-[[Category: Schonfeld, D L.]]
+</StructureSection>
-[[Category: Skerra, A.]]
+[[Category: Human]]
+[[Category: Large Structures]]
+[[Category: Mueller, U]]
+[[Category: Ravelli, R B.G]]
+[[Category: Schiefner, A]]
+[[Category: Schonfeld, D L]]
+[[Category: Skerra, A]]
 [[Category: Acute phase protein]]
 [[Category: Glycoprotein]]
 [[Category: Lipocalin]]
 [[Category: Plasma protein]]
+[[Category: Polymorphism]]
 [[Category: Pyrrolidone carboxylic acid]]
 [[Category: Secreted]]
 [[Category: Signaling protein]]