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.


3upe

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:05, 14 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor==
==Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor==
-
<StructureSection load='3upe' size='340' side='right' caption='[[3upe]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
+
<StructureSection load='3upe' size='340' side='right'caption='[[3upe]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3upe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UPE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UPE FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3upe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UPE FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0CA:1-[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL]-6-({1-[(1Z)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)-2-(PROPAN-2-YL)-1H-INDOLE-4-CARBOXYLIC+ACID'>0CA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 1.54&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1v2k|1v2k]], [[3unq|3unq]], [[3uns|3uns]], [[3unp|3unp]], [[3uqo|3uqo]], [[3uqv|3uqv]], [[3uqz|3uqz]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0CA:1-[(7-CARBAMIMIDOYLNAPHTHALEN-2-YL)METHYL]-6-({1-[(1Z)-ETHANIMIDOYL]PIPERIDIN-4-YL}OXY)-2-(PROPAN-2-YL)-1H-INDOLE-4-CARBOXYLIC+ACID'>0CA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=3upe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3upe OCA], [https://pdbe.org/3upe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3upe RCSB], [https://www.ebi.ac.uk/pdbsum/3upe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3upe ProSAT]</span></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3upe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3upe OCA], [http://pdbe.org/3upe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3upe RCSB], [http://www.ebi.ac.uk/pdbsum/3upe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3upe ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
-
Abstract A high-resolution crystallographic structure determination of a protein-ligand complex is generally accepted as the 'gold standard' for structure-based drug design, yet the relationship between structure and affinity is neither obvious nor straightforward. Here we analyze the interactions of a series of serine proteinase inhibitors with trypsin variants onto which the ligand-binding site of factor Xa has been grafted. Despite conservative mutations of only two residues not immediately in contact with ligands (second shell residues), significant differences in the affinity profiles of the variants are observed. Structural analyses demonstrate that these are due to multiple effects, including differences in the structure of the binding site, differences in target flexibility and differences in inhibitor binding modes. The data presented here highlight the myriad competing microscopic processes that contribute to protein-ligand interactions and emphasize the difficulties in predicting affinity from structure.
+
-
 
+
-
Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues.,Tziridis A, Rauh D, Neumann P, Kolenko P, Menzel A, Brauer U, Ursel C, Steinmetzer P, Sturzebecher J, Schweinitz A, Steinmetzer T, Stubbs MT Biol Chem. 2014 Jul 1;395(7-8):891-903. doi: 10.1515/hsz-2014-0158. PMID:25003390<ref>PMID:25003390</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3upe" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
-
*[[Trypsin|Trypsin]]
+
*[[Trypsin 3D structures|Trypsin 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bovin]]
+
[[Category: Bos taurus]]
-
[[Category: Trypsin]]
+
[[Category: Large Structures]]
-
[[Category: Kolenko, P]]
+
[[Category: Kolenko P]]
-
[[Category: Neumann, P]]
+
[[Category: Neumann P]]
-
[[Category: Stubbs, M T]]
+
[[Category: Stubbs MT]]
-
[[Category: Tziridis, A]]
+
[[Category: Tziridis A]]
-
[[Category: Duodenum]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Hydrolase-hydrolase inhibitor complex]]
+
-
[[Category: Protein binding]]
+
-
[[Category: Trypsin-like serine protease]]
+

Current revision

Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor

PDB ID 3upe

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/3upe"
Personal tools