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.


1pe6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1pe6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pe6, resolution 2.1&Aring;" /> '''REFINED X-RAY STRUCTU...)
Current revision (05:54, 17 April 2024) (edit) (undo)
 
(18 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1pe6.gif|left|200px]]<br /><applet load="1pe6" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1pe6, resolution 2.1&Aring;" />
 
-
'''REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION'''<br />
 
-
==Overview==
+
==REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION==
-
E-64-c, a synthetic cysteine protease inhibitor designed from E-64, binds, to papain through a thioether covalent bond. The x-ray diffraction data, for 2.1-A resolution were used to determine the three-dimensional, structure of this complex and refined it to R = 0.159. 0.159. In the, complex structure, the configurational conversion from S to R took place, on the epoxy carbon of E-64-c, implying that the nucleophilic attack of, the Cys-25 thiol group occurs at the opposite side of the epoxy oxygen, atom. The leucyl and isoamylamide groups of E-64-c were strongly fixed to, papain S subsites by specific interactions, including hydrogen bonding to, the Gly-66 residue. The carboxyl-terminal anion of E-64-c formed an, electrostatic interaction with the protonated His-159 imidazole ring, (O-...HN+ = 3.76 A) and consequently prevented the participation of this, residue in the hydrolytic charge-relay system. No significant distortion, caused by the binding of E-64-c was shown in the secondary structure of, papain. It is important to note that inhibitor and substrate have opposite, binding modes for the peptide groups. The possible relationship between, the binding mode and inhibitory activity is discussed on the basis of the, crystal structure of this complex.
+
<StructureSection load='1pe6' size='340' side='right'caption='[[1pe6]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1pe6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PE6 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]] 2.1&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</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=1pe6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pe6 OCA], [https://pdbe.org/1pe6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pe6 RCSB], [https://www.ebi.ac.uk/pdbsum/1pe6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pe6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PAPA1_CARPA PAPA1_CARPA]
 +
== 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/pe/1pe6_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=1pe6 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1PE6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with E6C and MOH as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.22.2 4.3.22.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PE6 OCA].
+
*[[Papain|Papain]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Refined x-ray structure of papain.E-64-c complex at 2.1-A resolution., Yamamoto D, Matsumoto K, Ohishi H, Ishida T, Inoue M, Kitamura K, Mizuno H, J Biol Chem. 1991 Aug 5;266(22):14771-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1860874 1860874]
+
[[Category: Carica papaya]]
-
[[Category: Lyase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Inoue M]]
-
[[Category: Inoue, M.]]
+
[[Category: Ishida T]]
-
[[Category: Ishida, T.]]
+
[[Category: Kitamura K]]
-
[[Category: Kitamura, K.]]
+
[[Category: Matsumoto K]]
-
[[Category: Matsumoto, K.]]
+
[[Category: Mizuno H]]
-
[[Category: Mizuno, H.]]
+
[[Category: Ohishi H]]
-
[[Category: Ohishi, H.]]
+
[[Category: Yamamoto D]]
-
[[Category: Yamamoto, D.]]
+
-
[[Category: E6C]]
+
-
[[Category: MOH]]
+
-
[[Category: hydrolase (sulfhydryl proteinase)]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:43:49 2007''
+

Current revision

REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION

PDB ID 1pe6

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/1pe6"
Personal tools