1ldn: Difference between revisions

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-[[Image:1ldn.gif|left|200px]]
- {{Structure
+==STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION==
-|PDB= 1ldn |SIZE=350|CAPTION= <scene name='initialview01'>1ldn</scene>, resolution 2.5&Aring;
+<StructureSection load='1ldn' size='340' side='right'caption='[[1ldn]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=FBP:FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OXM:OXAMIC+ACID'>OXM</scene>
+<table><tr><td colspan='2'>[[1ldn]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LDN FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span>
+</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>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OXM:OXAMIC+ACID'>OXM</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ldn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ldn OCA], [https://pdbe.org/1ldn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ldn RCSB], [https://www.ebi.ac.uk/pdbsum/1ldn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ldn ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ldn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ldn OCA], [http://www.ebi.ac.uk/pdbsum/1ldn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ldn RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/LDH_GEOSE LDH_GEOSE]
+== 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/ld/1ldn_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=1ldn ConSurf].
+<div style="clear:both"></div>
-'''STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION'''
+==See Also==
+*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-We report the refined structure of a ternary complex of an allosterically activated lactate dehydrogenase, including the important active site loop. Eightfold non-crystallographic symmetry averaging was utilized to improve the density maps. Interactions between the protein and bound coenzyme and oxamate are described in relation to other studies using site-specific mutagenesis. Fructose 1,6-bisphosphate (FruP2) is bound to the enzyme across one of the 2-fold axes of the tetramer, with the two phosphate moieties interacting with two anion binding sites, one on each of two subunits, across this interface. However, because FruP2 binds at this special site, yet does not possess an internal 2-fold symmetry axis, the ligand is statistically disordered and binds to each site in two different orientations. Binding of FruP2 to the tetramer is signalled to the active site principally through two interactions with His188 and Arg173. His188 is connected to His195 (which binds the carbonyl group of the substrate) and Arg173 is connected to Arg171 (the residue that binds the carboxylate group of the substrate).
-==About this Structure==
-LDN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDN OCA].
-==Reference==
-Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution., Wigley DB, Gamblin SJ, Turkenburg JP, Dodson EJ, Piontek K, Muirhead H, Holbrook JJ, J Mol Biol. 1992 Jan 5;223(1):317-35. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1731077 1731077]
 [[Category: Geobacillus stearothermophilus]]
-[[Category: L-lactate dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Dodson EJ]]
-[[Category: Dodson, E J.]]
+[[Category: Gamblin SJ]]
-[[Category: Gamblin, S J.]]
+[[Category: Holbrook JJ]]
-[[Category: Holbrook, J J.]]
+[[Category: Muirhead H]]
-[[Category: Muirhead, H.]]
+[[Category: Piontek K]]
-[[Category: Piontek, K.]]
+[[Category: Turkenburg JP]]
-[[Category: Turkenburg, J P.]]
+[[Category: Wigley DB]]
-[[Category: Wigley, D B.]]
-[[Category: oxidoreductase(choh(d)-nad(a))]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:01:31 2008''