This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1clz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:40, 13 March 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1clz.gif|left|200px]]<br /><applet load="1clz" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1clz, resolution 2.8&Aring;" />
 
-
'''IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER'''<br />
 
-
==Overview==
+
==IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER==
-
The crystal structures of the murine BR96 Fab and its human chimera have been determined in complex with the nonoate methyl ester derivative of Lewis Y (nLey) at 2.8 A and 2.5 A resolution, respectively. BR96 binds the carbohydrate in a large pocket which is formed by residues of all CDR loops except L2. The binding of the carbohydrate is mediated predominantly by aromatic residues in BR96. Analysis of the structure suggests that BR96 is capable of recognizing a structure larger than the Le(y) tetrasaccharide, providing a possible explanation for its high tumour selectivity. The structure provides a rationale for mutagenesis experiments that have resulted in BR96 CDR loop mutants with increased affinity for nLey and/or tumour cells.
+
<StructureSection load='1clz' size='340' side='right'caption='[[1clz]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1clz]] is a 2 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=1CLZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CLZ FirstGlance]. <br>
 +
</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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NON:METHYL+NONANOATE+(ESTER)'>NON</scene>, <scene name='pdbligand=PRD_900054:Lewis+Y+antigen,+beta+anomer'>PRD_900054</scene></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=1clz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1clz OCA], [https://pdbe.org/1clz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1clz RCSB], [https://www.ebi.ac.uk/pdbsum/1clz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1clz ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/IGHG3_MOUSE IGHG3_MOUSE]
 +
== 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/cl/1clz_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=1clz ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1CLZ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=NON:'>NON</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CLZ OCA].
+
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
The x-ray structure of an anti-tumour antibody in complex with antigen., Jeffrey PD, Bajorath J, Chang CY, Yelton D, Hellstrom I, Hellstrom KE, Sheriff S, Nat Struct Biol. 1995 Jun;2(6):466-71. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7664109 7664109]
+
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
-
[[Category: Protein complex]]
+
[[Category: Bajorath J]]
-
[[Category: Bajorath, J.]]
+
[[Category: Sheriff S]]
-
[[Category: Sheriff, S.]]
+
-
[[Category: NON]]
+
-
[[Category: glycoprotein]]
+
-
[[Category: immunoglobulin c region]]
+
-
[[Category: transmembrane]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:07:29 2008''
+

Current revision

IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER

PDB ID 1clz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1clz"
Personal tools