1k3d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:50, 16 August 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1k3d.png|left|200px]]
 
-
<!--
+
==Phosphoenolpyruvate carboxykinase in complex with ADP and AlF3==
-
The line below this paragraph, containing "STRUCTURE_1k3d", creates the "Structure Box" on the page.
+
<StructureSection load='1k3d' size='340' side='right'caption='[[1k3d]], [[Resolution|resolution]] 2.00&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'>[[1k3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K3D 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&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
{{STRUCTURE_1k3d| PDB=1k3d | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3d OCA], [https://pdbe.org/1k3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k3d RCSB], [https://www.ebi.ac.uk/pdbsum/1k3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3d ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PCKA_ECOLI PCKA_ECOLI]
 +
== 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/k3/1k3d_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=1k3d ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The mechanism of reversible transfer of the gamma-phosphate group of ATP by Escherichia coli phosphoenolpyruvate carboxykinase (PCK) on to its substrate is of great interest. It is known that metallofluorides are accurate analogs of the transition state in the context of kinase mechanisms. Therefore, two complexes of PCK, one with AlF(3), Mg(2+) and ADP (complex I), the other with AlF(3), Mg(2+), ADP and pyruvate (complex II) were crystallized. The X-ray crystal structures of these two complexes were determined at 2.0 A resolution. The Al atom has trigonal bipyramidal geometry that mimics the transition state of phosphoryl transfer. The Al atom is at a distance of 2.8 A and 2.9 A from an oxygen atom of the beta-phosphoryl group of ADP in complex I and II, respectively. A water molecule in complex I and an oxygen atom of the pyruvate in complex II are located along the axis of the trigonal bipyramid on the side opposite to the beta-phosphoryl oxygen with respect to the equatorial plane, suggesting that the complexes are close mimics of the transition state. Along with the presence of positively charged species around the AlF(3) moiety, these results indicate that phosphoryl transfer occurs via a direct displacement mechanism with associative qualities.
-
===Phosphoenolpyruvate carboxykinase in complex with ADP and AlF3===
+
The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3).,Sudom AM, Prasad L, Goldie H, Delbaere LT J Mol Biol. 2001 Nov 16;314(1):83-92. PMID:11724534<ref>PMID:11724534</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1k3d" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_11724534}}, adds the Publication Abstract to the page
+
*[[Phosphoenolpyruvate carboxykinase 3D structures|Phosphoenolpyruvate carboxykinase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 11724534 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_11724534}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
1K3D is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3D OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:11724534</ref><references group="xtra"/>
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Delbaere, L T.J.]]
+
[[Category: Large Structures]]
-
[[Category: Goldie, H.]]
+
[[Category: Delbaere LTJ]]
-
[[Category: Prasad, L.]]
+
[[Category: Goldie H]]
-
[[Category: Sudom, A M.]]
+
[[Category: Prasad L]]
-
[[Category: Gluconeogenesis]]
+
[[Category: Sudom AM]]
-
[[Category: Kinase]]
+
-
[[Category: Nucleotide-triphosphate hydrolase.]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:29:49 2009''
+

Current revision

Phosphoenolpyruvate carboxykinase in complex with ADP and AlF3

PDB ID 1k3d

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/1k3d"
Personal tools