This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3k2b

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3k2b" [edit=sysop:move=sysop])
Current revision (16:06, 1 November 2023) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3k2b.png|left|200px]]
 
-
<!--
+
==Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase complexed with NAD, from Arabidopsis thaliana==
-
The line below this paragraph, containing "STRUCTURE_3k2b", creates the "Structure Box" on the page.
+
<StructureSection load='3k2b' size='340' side='right'caption='[[3k2b]], [[Resolution|resolution]] 2.60&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'>[[3k2b]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K2B FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_3k2b| PDB=3k2b | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3k2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k2b OCA], [https://pdbe.org/3k2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k2b RCSB], [https://www.ebi.ac.uk/pdbsum/3k2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k2b ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/G3PA1_ARATH G3PA1_ARATH] Involved in the photosynthetic reductive pentose phosphate pathway (Calvin-Benson cycle). Catalyzes the reduction of 1,3-diphosphoglycerate by NADPH (By similarity).
 +
== 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/k2/3k2b_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=3k2b ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structure of the A(4) isoform of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Arabidopsis thaliana, expressed in recombinant form and complexed with NAD, is reported. The crystals, which were grown in 2.4 M ammonium sulfate and 0.1 M sodium citrate, belonged to space group I222. The asymmetric unit includes ten subunits, i.e. two independent tetramers plus a dimer that generates a third tetramer by a crystallographic symmetry operation. The crystal structure was solved by molecular replacement and refined to an R factor of 23.7% and an R(free) factor of 28.9% at 2.6 A resolution. In the final model, each subunit binds one NAD(+) molecule and two sulfates, which occupy the P(s) and the P(i) anion-binding sites. Detailed knowledge of this structure is instrumental for structural investigation of supramolecular complexes of A(4)-GAPDH, phosphoribulokinase and CP12, which are involved in the regulation of photosynthesis in the model plant A. thaliana.
-
===Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase complexed with NAD, from Arabidopsis thaliana===
+
Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform A4) from Arabidopsis thaliana in complex with NAD.,Fermani S, Sparla F, Marri L, Thumiger A, Pupillo P, Falini G, Trost P Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Jun 1;66(Pt 6):621-6. Epub, 2010 May 25. PMID:20516587<ref>PMID:20516587</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3k2b" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_20516587}}, adds the Publication Abstract to the page
+
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 20516587 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20516587}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[3k2b]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K2B OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:020516587</ref><ref group="xtra">PMID:016258009</ref><references group="xtra"/>
+
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
-
[[Category: Falini, G.]]
+
[[Category: Large Structures]]
-
[[Category: Fermani, S.]]
+
[[Category: Falini G]]
-
[[Category: Marri, L.]]
+
[[Category: Fermani S]]
-
[[Category: Sparla, F.]]
+
[[Category: Marri L]]
-
[[Category: Thumiger, A.]]
+
[[Category: Sparla F]]
-
[[Category: Trost, P.]]
+
[[Category: Thumiger A]]
-
[[Category: Calvin cycle]]
+
[[Category: Trost P]]
-
[[Category: Chloroplast]]
+
-
[[Category: Membrane]]
+
-
[[Category: Nadp]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Rossmann fold]]
+
-
[[Category: Transit peptide]]
+

Current revision

Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase complexed with NAD, from Arabidopsis thaliana

PDB ID 3k2b

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/3k2b"
Personal tools