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.


3f0t

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:40, 6 September 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3f0t.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with N-methyl-DHBT==
-
The line below this paragraph, containing "STRUCTURE_3f0t", creates the "Structure Box" on the page.
+
<StructureSection load='3f0t' size='340' side='right'caption='[[3f0t]], [[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'>[[3f0t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F0T 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=NCV:N-METHYL-6-(1,3-DIHYDROXY-ISOBUTYL)THYMINE'>NCV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_3f0t| PDB=3f0t | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3f0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0t OCA], [https://pdbe.org/3f0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f0t RCSB], [https://www.ebi.ac.uk/pdbsum/3f0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0t ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (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/f0/3f0t_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=3f0t ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Novel C-6 substituted pyrimidine derivatives are good substrates of herpes simplex virus type 1 thymidine kinase (HSV1-TK). Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-6-(1,3-dihydroxyisobutyl) thymine; N-Me DHBT), is phosphorylated at a similar rate compared to "gold standard" 9-[4-fluoro-3-(hydroxymethyl)butyl]guanine, FHBG, (K(m) = 10 +/- 0.3 muM; k(cat) = 0.036 +/- 0.015 sec(-1)). Additionally, it does not show cytotoxic properties on B16F1 cells up to a concentration of 10 mM. The x-ray analysis of the crystal structures of HSV1-TK with N-Me DHBT and of HSV1-TK with the fluorinated derivative N-Me FHBT confirmed the binding mode predicted by docking studies and their substrate characteristics. Moreover, the crystal structure of HSV1-TK with N-Me DHBT revealed an additional water-mediated H-bond interesting for the design of further analogues.
-
===Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with N-methyl-DHBT===
+
Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo.,Martic M, Pernot L, Westermaier Y, Perozzo R, Kraljevic TG, Kristafor S, Raic-Malic S, Scapozza L, Ametamey S Nucleosides Nucleotides Nucleic Acids. 2011 Apr;30(4):293-315. PMID:21623543<ref>PMID:21623543</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3f0t" style="background-color:#fffaf0;"></div>
-
==About this Structure==
+
==See Also==
-
3F0T is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Human_herpes_simplex_virus_type_1 Human herpes simplex virus type 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0T OCA].
+
*[[Thymidine kinase 3D structures|Thymidine kinase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:11056041</ref><ref group="xtra">PMID:7628623</ref><ref group="xtra">PMID:7552712</ref><references group="xtra"/>
+
__TOC__
-
[[Category: Human herpes simplex virus type 1]]
+
</StructureSection>
-
[[Category: Thymidine kinase]]
+
[[Category: Human alphaherpesvirus 1 strain 17]]
-
[[Category: Ametamey, S.]]
+
[[Category: Large Structures]]
-
[[Category: Martic, M.]]
+
[[Category: Ametamey S]]
-
[[Category: Pernot, L.]]
+
[[Category: Martic M]]
-
[[Category: Perozzo, R.]]
+
[[Category: Pernot L]]
-
[[Category: Scapozza, L.]]
+
[[Category: Perozzo R]]
-
[[Category: Atp-binding]]
+
[[Category: Scapozza L]]
-
[[Category: Dna synthesis]]
+
[[Category: Westermaier Y]]
-
[[Category: Dna-synthesis]]
+
-
[[Category: Early protein]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Pet tracer]]
+
-
[[Category: Thymidine kinase]]
+
-
[[Category: Transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 4 10:54:39 2009''
+

Current revision

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with N-methyl-DHBT

PDB ID 3f0t

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/3f0t"
Personal tools