3a3f: Difference between revisions

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-{{Seed}}
-[[Image:3a3f.jpg|left|200px]]
-<!--
+==Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae,complexed with novel beta-lactam (FMZ)==
-The line below this paragraph, containing "STRUCTURE_3a3f", creates the "Structure Box" on the page.
+<StructureSection load='3a3f' size='340' side='right'caption='[[3a3f]], [[Resolution|resolution]] 2.10&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'>[[3a3f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A3F FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMZ:(2R,4S)-5,5-DIMETHYL-2-[(1R)-2-OXO-1-({(2R)-2-[(2-OXOIMIDAZOLIDIN-1-YL)AMINO]-2-PHENYLACETYL}AMINO)ETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC+ACID'>FMZ</scene></td></tr>
--->
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a3d|3a3d]], [[3a3e|3a3e]], [[3a3i|3a3i]], [[3a3j|3a3j]]</div></td></tr>
-{{STRUCTURE_3a3f|  PDB=3a3f  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dacB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=3a3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a3f OCA], [https://pdbe.org/3a3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a3f RCSB], [https://www.ebi.ac.uk/pdbsum/3a3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a3f ProSAT]</span></td></tr>
+</table>
+== 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/a3/3a3f_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=3a3f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have determined high-resolution apo crystal structures of two low molecular weight penicillin-binding proteins (PBPs), PBP4 and PBP5, from Haemophilus influenzae, one of the most frequently found pathogens in the upper respiratory tract of children. Novel beta-lactams with notable antimicrobial activity have been designed, and crystal structures of PBP4 complexed with ampicillin and two of the novel molecules have also been determined. Comparing the apo form with those of the complexes, we find that the drugs disturb the PBP4 structure and weaken X-ray diffraction, to very different extents. PBP4 has recently been shown to act as a sensor of the presence of penicillins in Pseudomonas aeruginosa, and our models offer a clue to the structural basis for this effect. Covalently attached penicillins press against a phenylalanine residue near the active site and disturb the deacylation step. The ready inhibition of PBP4 by beta-lactams compared to PBP5 also appears to be related to the weaker interactions holding key residues in a catalytically competent position.
-===Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae,complexed with novel beta-lactam (FMZ)===
+Crystal structures of penicillin-binding proteins 4 and 5 from Haemophilus influenzae.,Kawai F, Clarke TB, Roper DI, Han GJ, Hwang KY, Unzai S, Obayashi E, Park SY, Tame JR J Mol Biol. 2010 Feb 26;396(3):634-45. Epub 2009 Dec 1. PMID:19958776<ref>PMID:19958776</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3a3f" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19958776}}, adds the Publication Abstract to the page
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19958776 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19958776}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacterium influenzae lehmann and neumann 1896]]
-A3F is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A3F OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:19958776</ref><references group="xtra"/>
-[[Category: Haemophilus influenzae]]
 [[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-[[Category: Kawai, F.]]
+[[Category: Kawai, F]]
-[[Category: Park, S Y.]]
+[[Category: Park, S Y]]
-[[Category: Roper, D I.]]
+[[Category: Roper, D I]]
-[[Category: Tame, J R.H.]]
+[[Category: Tame, J R.H]]
 [[Category: Dacb]]
 [[Category: Hydrolase]]
 [[Category: Pbp4]]
 [[Category: Penicillin binding protein 4]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Dec 24 07:37:56 2009''