3kb6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (16:10, 1 November 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3kb6.png|left|200px]]
 
-
{{STRUCTURE_3kb6| PDB=3kb6 | SCENE= }}
+
==Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid==
 +
<StructureSection load='3kb6' size='340' side='right'caption='[[3kb6]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3kb6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pi1 2pi1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KB6 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]] 2.12&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</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=3kb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kb6 OCA], [https://pdbe.org/3kb6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kb6 RCSB], [https://www.ebi.ac.uk/pdbsum/3kb6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kb6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/O66939_AQUAE O66939_AQUAE]
 +
== 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/kb/3kb6_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=3kb6 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structure of D-lactate dehydrogenase from Aquifex aeolicus (aq_727) was determined to 2.12 A resolution in space group P2(1)2(1)2(1), with unit-cell parameters a = 90.94, b = 94.43, c = 188.85 A. The structure was solved by molecular replacement using the coenzyme-binding domain of Lactobacillus helveticus D-lactate dehydrogenase and contained two homodimers in the asymmetric unit. Each subunit of the homodimer was found to be in a ;closed' conformation with the NADH cofactor bound to the coenzyme-binding domain and with a lactate (or pyruvate) molecule bound at the interdomain active-site cleft.
-
===Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid===
+
Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).,Antonyuk SV, Strange RW, Ellis MJ, Bessho Y, Kuramitsu S, Inoue Y, Yokoyama S, Hasnain SS Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Dec 1;65(Pt, 12):1209-13. Epub 2009 Nov 27. PMID:20054113<ref>PMID:20054113</ref>
-
{{ABSTRACT_PUBMED_20054113}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 3kb6" style="background-color:#fffaf0;"></div>
-
[[3kb6]] is a 4 chain structure of [[Lactate Dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pi1 2pi1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KB6 OCA].
+
==See Also==
==See Also==
-
*[[Lactate Dehydrogenase|Lactate Dehydrogenase]]
+
*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:020054113</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
-
[[Category: D-lactate dehydrogenase]]
+
[[Category: Large Structures]]
-
[[Category: Antonyuk, S V.]]
+
[[Category: Antonyuk SV]]
-
[[Category: Bessho, Y.]]
+
[[Category: Bessho Y]]
-
[[Category: Ellis, M J.]]
+
[[Category: Ellis MJ]]
-
[[Category: Hasnain, S S.]]
+
[[Category: Hasnain SS]]
-
[[Category: Kuramitsu, S.]]
+
[[Category: Kuramitsu S]]
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
[[Category: Strange RW]]
-
[[Category: Strange, R W.]]
+
[[Category: Yokoyama S]]
-
[[Category: Yokoyama, S.]]
+
-
[[Category: D-ldh]]
+
-
[[Category: Nad]]
+
-
[[Category: National project on protein structural and functional analyse]]
+
-
[[Category: Nppsfa]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Riken structural genomics/proteomics initiative]]
+
-
[[Category: Rsgi]]
+
-
[[Category: Structural genomic]]
+

Current revision

Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid

PDB ID 3kb6

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3kb6"
Personal tools