1ifh: Difference between revisions

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-{{Seed}}
-[[Image:1ifh.png|left|200px]]
-<!--
+==A DETAILED ANALYSIS OF THE FREE AND BOUND CONFORMATION OF AN ANTIBODY: X-RAY STRUCTURES OF ANTI-PEPTIDE FAB 17(SLASH)9 AND THREE DIFFERENT FAB-PEPTIDE COMPLEXES==
-The line below this paragraph, containing "STRUCTURE_1ifh", creates the "Structure Box" on the page.
+<StructureSection load='1ifh' size='340' side='right'caption='[[1ifh]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1ifh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IFH FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
-{{STRUCTURE_1ifh|  PDB=1ifh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ifh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifh OCA], [https://pdbe.org/1ifh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ifh RCSB], [https://www.ebi.ac.uk/pdbsum/1ifh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ifh ProSAT]</span></td></tr>
+</table>
+== 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/if/1ifh_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=1ifh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A new orthorhombic crystal form of Fab 17/9 has been determined in complex with a 7-mer peptide from influenza virus hemagglutinin (HA1 101-107, acetylated and amidated). The three-dimensional structure was resolved to 2.8 A with an improved refinement and better geometry than two previously determined Fab 17/9-peptide (HA1 100-108) complexes, facilitating a detailed description of the Fab-peptide interactions. The binding pockets and the peptide antigen are structurally similar in all three peptide complexes of Fab 17/9. The peptide adopts an extended conformation (residues 100 to 103) and a type I reverse turn (residues 104 to 107). Additionally, the antigenic determinant described here correlates well with previous epitope mapping studies. The structures of the free and antigen bound Fab illustrate the role of induced fit as a mechanism for antibody-antigen recognition. Fab 17/9 undergoes a large conformational change, mainly in the H3 loop, upon peptide binding. As a result, the shape of the binding pocket changes substantially in the liganded Fab. However, the backbone conformations of the other hypervariable loops (L2, L3, H1 and H2) show no significant difference between free and bound structures. The conformation of the L1 loop is also maintained in all structures, but its position relative to the framework varies in different crystal environments. The availability of three X-ray structures of an Fab-peptide complex in three different space groups makes it possible to clearly distinguish between crystal packing and antigen binding as the cause of structural differences. Two distinct H3-loop conformations, free and bound, are observed with no evidence otherwise for multiple conformations of the hypervariable loops (CDRs) or increased flexibility in either the free or bound forms.
-===A DETAILED ANALYSIS OF THE FREE AND BOUND CONFORMATION OF AN ANTIBODY: X-RAY STRUCTURES OF ANTI-PEPTIDE FAB 17(SLASH)9 AND THREE DIFFERENT FAB-PEPTIDE COMPLEXES===
+Detailed analysis of the free and bound conformations of an antibody. X-ray structures of Fab 17/9 and three different Fab-peptide complexes.,Schulze-Gahmen U, Rini JM, Wilson IA J Mol Biol. 1993 Dec 20;234(4):1098-118. PMID:8263915<ref>PMID:8263915</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ifh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_8263915}}, adds the Publication Abstract to the page
+*[[Antibody 3D structures|Antibody 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 8263915 is the PubMed ID number.
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
--->
+== References ==
-{{ABSTRACT_PUBMED_8263915}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-IFH is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFH OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:8263915</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Schulze-Gahmen, U.]]
+[[Category: Schulze-Gahmen U]]
-[[Category: Wilson, I A.]]
+[[Category: Wilson IA]]
-[[Category: Immunoglobulin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 19:40:44 2009''