3kjd: Difference between revisions

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-[[Image:3kjd.png|left|200px]]
-{{STRUCTURE_3kjd|  PDB=3kjd  |  SCENE=  }}
+==Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888==
+<StructureSection load='3kjd' size='340' side='right'caption='[[3kjd]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3kjd]] is a 2 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=3KJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KJD 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]] 1.95&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=78P:(2R)-2-(7-CARBAMOYL-1H-BENZIMIDAZOL-2-YL)-2-METHYLPYRROLIDINIUM'>78P</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=3kjd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kjd OCA], [https://pdbe.org/3kjd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kjd RCSB], [https://www.ebi.ac.uk/pdbsum/3kjd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kjd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PARP2_HUMAN PARP2_HUMAN] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks.
+== 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/kj/3kjd_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=3kjd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Poly-ADP-ribose polymerases (PARPs) catalyze transfer of ADP-ribose from NAD(+) to specific residues in their substrate proteins or to growing ADP-ribose chains. PARP activity is involved in processes such as chromatin remodeling, transcription control, and DNA repair. Inhibitors of PARP activity may be useful in cancer therapy. PARP2 is the family member that is most similar to PARP1, and the two can act together as heterodimers. We used X-ray crystallography to determine two structures of the catalytic domain of human PARP2: the complexes with PARP inhibitors 3-aminobenzamide and ABT-888. These results contribute to our understanding of structural features and compound properties that can be employed to develop selective inhibitors of human ADP-ribosyltransferases.
-===Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888===
+Crystal structure of the catalytic domain of human PARP2 in complex with PARP inhibitor ABT-888.,Karlberg T, Hammarstrom M, Schutz P, Svensson L, Schuler H Biochemistry. 2010 Feb 16;49(6):1056-8. PMID:20092359<ref>PMID:20092359</ref>
-{{ABSTRACT_PUBMED_20092359}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3kjd" style="background-color:#fffaf0;"></div>
-[[3kjd]] is a 2 chain structure of [[Poly (ADP-ribose) polymerase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KJD OCA].
 ==See Also==
-*[[Poly (ADP-ribose) polymerase|Poly (ADP-ribose) polymerase]]
+*[[Poly(ADP-ribose) polymerase 3D structures|Poly(ADP-ribose) polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020092359</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Large Structures]]
-[[Category: Berg, S Van Den.]]
+[[Category: Arrowsmith CH]]
-[[Category: Berglund, H.]]
+[[Category: Berglund H]]
-[[Category: Bountra, C.]]
+[[Category: Bountra C]]
-[[Category: Collins, R.]]
+[[Category: Collins R]]
-[[Category: Edwards, A M.]]
+[[Category: Edwards AM]]
-[[Category: Flodin, S.]]
+[[Category: Flodin S]]
-[[Category: Flores, A.]]
+[[Category: Flores A]]
-[[Category: Graslund, S.]]
+[[Category: Graslund S]]
-[[Category: Hammarstrom, M.]]
+[[Category: Hammarstrom M]]
-[[Category: Johansson, A.]]
+[[Category: Johansson A]]
-[[Category: Johansson, I.]]
+[[Category: Johansson I]]
-[[Category: Kallas, A.]]
+[[Category: Kallas A]]
-[[Category: Karlberg, T.]]
+[[Category: Karlberg T]]
-[[Category: Kotenyova, T.]]
+[[Category: Kotenyova T]]
-[[Category: Kotzsch, A.]]
+[[Category: Kotzsch A]]
-[[Category: Kraulis, P.]]
+[[Category: Kraulis P]]
-[[Category: Moche, M.]]
+[[Category: Moche M]]
-[[Category: Nielsen, T K.]]
+[[Category: Nielsen TK]]
-[[Category: Nordlund, P.]]
+[[Category: Nordlund P]]
-[[Category: Nyman, T.]]
+[[Category: Nyman T]]
-[[Category: Persson, C.]]
+[[Category: Persson C]]
-[[Category: Roos, A K.]]
+[[Category: Roos AK]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Schuler H]]
-[[Category: Schuler, H.]]
+[[Category: Schutz P]]
-[[Category: Schutz, P.]]
+[[Category: Siponen MI]]
-[[Category: Siponen, M I.]]
+[[Category: Thorsell AG]]
-[[Category: Thorsell, A G.]]
+[[Category: Tresaugues L]]
-[[Category: Tresaugues, L.]]
+[[Category: Van Den Berg S]]
-[[Category: Weigelt, J.]]
+[[Category: Weigelt J]]
-[[Category: Welin, M.]]
+[[Category: Welin M]]
-[[Category: Wisniewska, M.]]
+[[Category: Wisniewska M]]
-[[Category: Catalytic fragment]]
-[[Category: Dna-binding]]
-[[Category: Enzyme-inhibitor complex]]
-[[Category: Glycosyltransferase]]
-[[Category: Nad]]
-[[Category: Nucleus]]
-[[Category: Sgc]]
-[[Category: Structural genomic]]
-[[Category: Structural genomics consortium]]
-[[Category: Transferase]]