2a8g

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:48, 30 October 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2a8g.png|left|200px]]
 
-
<!--
+
==Structure of Avidin in complex with the ligand deoxyguanosine==
-
The line below this paragraph, containing "STRUCTURE_2a8g", creates the "Structure Box" on the page.
+
<StructureSection load='2a8g' size='340' side='right'caption='[[2a8g]], [[Resolution|resolution]] 1.99&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'>[[2a8g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A8G 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]] 1.99&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-
{{STRUCTURE_2a8g| PDB=2a8g | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2a8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8g OCA], [https://pdbe.org/2a8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a8g RCSB], [https://www.ebi.ac.uk/pdbsum/2a8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a8g ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/AVID_CHICK AVID_CHICK] The biological function of avidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of avidin).
 +
== 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/a8/2a8g_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2a8g ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Oxidative damage of DNA results in the formation of many products, including 8-oxodeoxyguanosine, which has been used as a marker to quantify DNA damage. Earlier studies have demonstrated that avidin, a protein prevalent in egg-white and which has high affinity for the vitamin biotin, binds to 8-oxodeoxyguanosine and related bases. In this study, we have determined crystal structures of avidin in complex with 8-oxodeoxyguanosine and 8-oxodeoxyadenosine. In each case, the base is observed to bind within the biotin-binding site of avidin. However, the mode of association between the bases and the protein varies and, unlike in the avidin:biotin complex, complete ordering of the protein in this region does not accompany binding. Fluorescence studies indicate that in solution the individual bases, and a range of oligonucleotides, bind to avidin with micromolar affinity. Only one of the modes of binding observed is consistent with recognition of oxidised purines when incorporated within a DNA oligomer, and from this structure a model is proposed for the selective binding of avidin to DNA containing oxidatively damaged deoxyguanosine. These studies illustrate the molecular basis by which avidin might act as a marker of DNA damage, although the low levels of binding observed are inconsistent with the recognition of oxidised purines forming a major physiological role for avidin.
-
===Structure of Avidin in complex with the ligand deoxyguanosine===
+
Recognition of oxidatively modified bases within the biotin-binding site of avidin.,Conners R, Hooley E, Clarke AR, Thomas S, Brady RL J Mol Biol. 2006 Mar 17;357(1):263-74. Epub 2006 Jan 6. PMID:16413579<ref>PMID:16413579</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2a8g" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_16413579}}, adds the Publication Abstract to the page
+
*[[Avidin 3D structures|Avidin 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 16413579 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_16413579}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2A8G is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8G OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:16413579</ref><references group="xtra"/>
+
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
-
[[Category: Brady, R L.]]
+
[[Category: Large Structures]]
-
[[Category: Conners, R.]]
+
[[Category: Brady RL]]
-
[[Category: Hooley, E.]]
+
[[Category: Conners R]]
-
[[Category: Thomas, S.]]
+
[[Category: Hooley E]]
-
[[Category: Beta barrel]]
+
[[Category: Thomas S]]
-
[[Category: Unknown function]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 8 12:49:46 2009''
+

Current revision

Structure of Avidin in complex with the ligand deoxyguanosine

PDB ID 2a8g

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/2a8g"
Personal tools