1kcr: Difference between revisions

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<StructureSection load='1kcr' size='340' side='right'caption='[[1kcr]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<StructureSection load='1kcr' size='340' side='right'caption='[[1kcr]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1kcr]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KCR FirstGlance]. <br>
<table><tr><td colspan='2'>[[1kcr]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepatitis_B_virus_genotype_A1_subtype_adw2_(Isolate_South_Africa/84/2001) Hepatitis B virus genotype A1 subtype adw2 (Isolate South Africa/84/2001)] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KCR FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kc5|1kc5]], [[1kcs|1kcs]], [[1kcu|1kcu]], [[1kcv|1kcv]]</div></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]] 2.9&#8491;</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=1kcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kcr OCA], [https://pdbe.org/1kcr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kcr RCSB], [https://www.ebi.ac.uk/pdbsum/1kcr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kcr 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=1kcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kcr OCA], [https://pdbe.org/1kcr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kcr RCSB], [https://www.ebi.ac.uk/pdbsum/1kcr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kcr ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IGKC_MOUSE IGKC_MOUSE]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1kcr ConSurf].
</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=1kcr ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of Fab of an Ab PC283 complexed with its corresponding peptide Ag, PS1 (HQLDPAFGANSTNPD), derived from the hepatitis B virus surface Ag was determined. The PS1 stretch Gln2P to Phe7P is present in the Ag binding site of the Ab, while the next three residues of the peptide are raised above the binding groove. The residues Ser11P, Thr12P, and Asn13P then loop back onto the Ag-binding site of the Ab. The last two residues, Pro14P and Asp15P, extend outside the binding site without forming any contacts with the Ab. The PC283-PS1 complex is among the few examples where the light chain complementarity-determining regions show more interactions than the heavy chain complementarity-determining regions, and a distal framework residue is involved in Ag binding. As seen from the crystal structure, most of the contacts between peptide and Ab are through the five residues, Leu3-Asp4-Pro5-Ala6-Phe7, of PS1. The paratope is predominantly hydrophobic with aromatic residues lining the binding pocket, although a salt bridge also contributes to stabilizing the Ag-Ab interaction. The molecular surface area buried upon PS1 binding is 756 A(2) for the peptide and 625 A(2) for the Fab, which is higher than what has been seen to date for Ab-peptide complexes. A comparison between PC283 structure and a homology model of its germline ancestor suggests that paratope optimization for PS1 occurs by improving both charge and shape complementarity.
Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition.,Nair DT, Singh K, Sahu N, Rao KV, Salunke DM J Immunol. 2000 Dec 15;165(12):6949-55. PMID:11120821<ref>PMID:11120821</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1kcr" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lk3 transgenic mice]]
[[Category: Mus musculus]]
[[Category: Nair, D T]]
[[Category: Nair DT]]
[[Category: Rao, K V.S]]
[[Category: Rao KVS]]
[[Category: Sahu, N]]
[[Category: Sahu N]]
[[Category: Salunke, D M]]
[[Category: Salunke DM]]
[[Category: Singh, K]]
[[Category: Singh K]]
[[Category: Antibody]]
[[Category: Immune system]]

Revision as of 10:59, 3 April 2024

CRYSTAL STRUCTURE OF ANTIBODY PC283 IN COMPLEX WITH PS1 PEPTIDECRYSTAL STRUCTURE OF ANTIBODY PC283 IN COMPLEX WITH PS1 PEPTIDE

Structural highlights

1kcr is a 3 chain structure with sequence from Hepatitis B virus genotype A1 subtype adw2 (Isolate South Africa/84/2001) and Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IGKC_MOUSE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1kcr, resolution 2.90Å

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OCA
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