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.


1mcj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:34, 10 April 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1mcj.jpg|left|200px]]
 
-
<!--
+
==PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS==
-
The line below this paragraph, containing "STRUCTURE_1mcj", creates the "Structure Box" on the page.
+
<StructureSection load='1mcj' size='340' side='right'caption='[[1mcj]], [[Resolution|resolution]] 2.70&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'>[[1mcj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MCJ 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]] 2.7&#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>, <scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene>, <scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-
{{STRUCTURE_1mcj| PDB=1mcj | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mcj OCA], [https://pdbe.org/1mcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mcj RCSB], [https://www.ebi.ac.uk/pdbsum/1mcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mcj ProSAT]</span></td></tr>
-
 
+
</table>
-
'''PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS'''
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
==Overview==
+
<jmolCheckbox>
-
An immunoglobulin light chain dimer with a large generic binding cavity was used as a host molecule for designing a series of peptide guest ligands. In a screening procedure peptides coupled to solid supports were systematically tested for binding activity by enzyme linked immunosorbent assays (ELISA). Key members of the binding series were synthesized in milligram quantities and diffused into crystals of the host molecule for X-ray analyses. These peptides were incrementally increased in size and affinity until they nearly filled the cavity. Progressive changes in binding patterns were mapped by comparisons of crystallographically refined structures of 14 peptide-protein complexes at 2.7 A resolution. These comparisons led to guidelines for ligand design and also suggested ways to modify previously established binding patterns. By manipulating equilibria involving histidine, for example, it was possible to abolish one important intramolecular interaction of the bound ligand and substitute another. These events triggered a change in conformation of the ligand from a compact to an extended form and a comprehensive change in the mode of binding to the protein. In dipeptides of histidine and proline, protonation of both imidazolium nitrogen atoms was used to program an end-to-end reversal of the direction in which the ligand was inserted into the binding cavity. Peptides cocrystallized with proteins produced complexes somewhat different in structure from those in which ligands were diffused into preexisting crystals. In such a large and malleable cavity, space utilization was thus different when a ligand was introduced before the imposition of crystal packing restraints.
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mc/1mcj_consurf.spt"</scriptWhenChecked>
-
 
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
==About this Structure==
+
<text>to colour the structure by Evolutionary Conservation</text>
-
1MCJ is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MCJ OCA].
+
</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=1mcj ConSurf].
-
==Reference==
+
<div style="clear:both"></div>
-
Principles and pitfalls in designing site-directed peptide ligands., Edmundson AB, Harris DL, Fan ZC, Guddat LW, Schley BT, Hanson BL, Tribbick G, Geysen HM, Proteins. 1993 Jul;16(3):246-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8346191 8346191]
+
__TOC__
-
[[Category: Single protein]]
+
</StructureSection>
-
[[Category: Edmundson, A B.]]
+
[[Category: Homo sapiens]]
-
[[Category: Fan, Z C.]]
+
[[Category: Large Structures]]
-
[[Category: Guddat, L W.]]
+
[[Category: Edmundson AB]]
-
[[Category: Harris, D L.]]
+
[[Category: Fan Z-C]]
-
[[Category: Immunoglobulin]]
+
[[Category: Guddat LW]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 00:53:22 2008''
+
[[Category: Harris DL]]

Current revision

PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS

PDB ID 1mcj

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/1mcj"
Personal tools