1krm: Difference between revisions

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-[[Image:1krm.jpg|left|200px]]
-<!--
+==Crystal structure of bovine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine riboside==
-The line below this paragraph, containing "STRUCTURE_1krm", creates the "Structure Box" on the page.
+<StructureSection load='1krm' size='340' side='right'caption='[[1krm]], [[Resolution|resolution]] 2.50&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'>[[1krm]] 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=1KRM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KRM 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PRH:6-HYDROXY-1,6-DIHYDRO+PURINE+NUCLEOSIDE'>PRH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1krm|  PDB=1krm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1krm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1krm OCA], [https://pdbe.org/1krm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1krm RCSB], [https://www.ebi.ac.uk/pdbsum/1krm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1krm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADA_BOVIN ADA_BOVIN] Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. Plays an important role in purine metabolism and in adenosine homeostasis. Modulates signaling by extracellular adenosine, and so contributes indirectly to cellular signaling events. Acts as a positive regulator of T-cell coactivation, by binding DPP4. Its interaction with DPP4 regulates lymphocyte-epithelial cell adhesion (By similarity).
+== 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/kr/1krm_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=1krm ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of bovine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine riboside'''
+==See Also==
+*[[Adenosine deaminase 3D structures|Adenosine deaminase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The crystal structure of adenosine deaminase (ADA) from bovine intestine complexed with a transition-state analogue, 6-hydroxy-1,6-dihydropurine riboside (HDPR), was solved at 2.5 A resolution by the molecular-replacement method using a homology model based on the crystal structure of mouse ADA. The final refinement converged to a crystallographic R factor of 20.7%. The C(alpha) backbone of bovine ADA is mostly superimposable on that of mouse ADA, although mouse ADA itself did not lead to a solution by molecular replacement. HDPR tightly interacts with ADA by means of six hydrogen bonds and is entirely enclosed within the active site. The lid of the envelope consists of two components: one contains two leucine residues, Leu55 and Leu59, and the other contains the backbone atoms Asp182 and Glu183. The C(delta) atoms of the two leucine residues are 3.5 A from the respective N atoms of the backbone. A weak interaction, similar to CH-pi binding, might make it possible to open the lid. Taking account of the movement and observation of this structural feature, the aim is to design novel ADA inhibitors.
-==About this Structure==
-KRM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KRM OCA].
-==Reference==
-Structure of bovine adenosine deaminase complexed with 6-hydroxy-1,6-dihydropurine riboside., Kinoshita T, Nishio N, Nakanishi I, Sato A, Fujii T, Acta Crystallogr D Biol Crystallogr. 2003 Feb;59(Pt 2):299-303. Epub 2003, Jan 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12554940 12554940]
-[[Category: Adenosine deaminase]]
 [[Category: Bos taurus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Kinoshita, T.]]
+[[Category: Kinoshita T]]
-[[Category: Adenosine deaminase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 23:05:14 2008''