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.


3fkb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3fkb" [edit=sysop:move=sysop])
Current revision (15:30, 1 November 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3fkb.png|left|200px]]
 
-
<!--
+
==Structure of NDPK H122G and tenofovir-diphosphate==
-
The line below this paragraph, containing "STRUCTURE_3fkb", creates the "Structure Box" on the page.
+
<StructureSection load='3fkb' size='340' side='right'caption='[[3fkb]], [[Resolution|resolution]] 1.65&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'>[[3fkb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FKB 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]] 1.65&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TNM:[(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-2-YL]OXYMETHYL-PHOSPHONOOXY-PHOSPHINIC+ACID'>TNM</scene>, <scene name='pdbligand=TNV:[2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE'>TNV</scene></td></tr>
-
{{STRUCTURE_3fkb| PDB=3fkb | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fkb OCA], [https://pdbe.org/3fkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fkb RCSB], [https://www.ebi.ac.uk/pdbsum/3fkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fkb ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
 +
== 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/fk/3fkb_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=3fkb ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Tenofovir is an acyclic phosphonate analog of deoxyadenylate used in AIDS and hepatitis B therapy. We find that tenofovir diphosphate, its active form, can be produced by human nucleoside diphosphate kinase (NDPK), but with low efficiency, and that creatine kinase is significantly more active. The 1.65 A x-ray structure of NDPK in complex with tenofovir mono- and diphosphate shows that the analogs bind at the same site as natural nucleotides, but in a different conformation, and make only a subset of the Van der Waals and polar interactions made by natural substrates, consistent with their comparatively low affinity for the enzyme.
-
===Structure of NDPK H122G and tenofovir-diphosphate===
+
Nucleoside diphosphate kinase and the activation of antiviral phosphonate analogs of nucleotides: binding mode and phosphorylation of tenofovir derivatives.,Koch K, Chen Y, Feng JY, Borroto-Esoda K, Deville-Bonne D, Gallois-Montbrun S, Janin J, Morera S Nucleosides Nucleotides Nucleic Acids. 2009 Aug;28(8):776-92. PMID:20183617<ref>PMID:20183617</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_20183617}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3fkb" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20183617 is the PubMed ID number.
+
-
-->
+
-
{{ABSTRACT_PUBMED_20183617}}
+
-
 
+
-
==About this Structure==
+
-
[[3fkb]] is a 6 chain structure of [[Nucleoside diphosphate kinase]] with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FKB OCA].
+
==See Also==
==See Also==
-
*[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]]
+
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:020183617</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
[[Category: Dictyostelium discoideum]]
[[Category: Dictyostelium discoideum]]
-
[[Category: Nucleoside-diphosphate kinase]]
+
[[Category: Large Structures]]
-
[[Category: Chen, Y X.]]
+
[[Category: Chen YX]]
-
[[Category: Morera, S.]]
+
[[Category: Morera S]]
-
[[Category: An hexamer structure]]
+
-
[[Category: Atp-binding]]
+
-
[[Category: Kinase]]
+
-
[[Category: Magnesium]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Nucleotide metabolism]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Phosphoprotein]]
+
-
[[Category: Transferase]]
+

Current revision

Structure of NDPK H122G and tenofovir-diphosphate

PDB ID 3fkb

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/3fkb"
Personal tools