3td5: Difference between revisions

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 ==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala==
-<StructureSection load='3td5' size='340' side='right' caption='[[3td5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3td5' size='340' side='right'caption='[[3td5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3td3|3td3]], [[3td4|3td4]]</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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [https://pdbe.org/3td5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [https://www.ebi.ac.uk/pdbsum/3td5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3td5 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">omp38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 Acinetobacter baumannii])</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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [http://www.ebi.ac.uk/pdbsum/3td5 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/OMP38_ACIB2 OMP38_ACIB2] Functions as a porin (PubMed:9928952). Induces apoptosis in human cell lines through caspase-dependent and AIF-dependent pathways. Purified Omp38 enters host cell and localizes to the mitochondria, which presumably leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor) (PubMed:16008580). Binds peptidoglycan, contributes to cell wall maintenance (Probable).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref> <ref>PMID:16008580</ref> <ref>PMID:21965596</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3td5" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Acinetobacter baumannii]]
-[[Category: Kim, H Y]]
+[[Category: Large Structures]]
-[[Category: Lee, W C]]
+[[Category: Kim HY]]
-[[Category: Park, J S]]
+[[Category: Lee WC]]
-[[Category: Song, J H]]
+[[Category: Park JS]]
-[[Category: Cell-wall attachment]]
+[[Category: Song JH]]
-[[Category: Membrane protein-peptide binding protein complex]]
-[[Category: Ompa-like fold]]
-[[Category: Peptidoglycan-binding]]