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.


2vgd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:07, 1 May 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2vgd.png|left|200px]]
 
-
<!--
+
==Crystal structure of environmental isolated GH11 in complex with xylobiose and feruloyl-arabino-xylotriose==
-
The line below this paragraph, containing "STRUCTURE_2vgd", creates the "Structure Box" on the page.
+
<StructureSection load='2vgd' size='340' side='right'caption='[[2vgd]], [[Resolution|resolution]] 1.80&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'>[[2vgd]] 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=2VGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VGD 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]] 1.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FX3:5-O-[(2E)-3-(4-HYDROXY-3-METHOXYPHENYL)PROP-2-ENOYL]-ALPHA-L-RIBOFURANOSE'>FX3</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</scene>, <scene name='pdbligand=PRD_900117:4beta-beta-xylotriose'>PRD_900117</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-
{{STRUCTURE_2vgd| PDB=2vgd | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgd OCA], [https://pdbe.org/2vgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vgd RCSB], [https://www.ebi.ac.uk/pdbsum/2vgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgd ProSAT]</span></td></tr>
-
 
+
</table>
-
===CRYSTAL STRUCTURE OF ENVIRONMENTAL ISOLATED GH11 IN COMPLEX WITH XYLOBIOSE AND FERULOYL-ARABINO-XYLOTRIOSE===
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
<!--
+
<jmolCheckbox>
-
The line below this paragraph, {{ABSTRACT_PUBMED_18078955}}, adds the Publication Abstract to the page
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vg/2vgd_consurf.spt"</scriptWhenChecked>
-
(as it appears on PubMed at http://www.pubmed.gov), where 18078955 is the PubMed ID number.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
-->
+
<text>to colour the structure by Evolutionary Conservation</text>
-
{{ABSTRACT_PUBMED_18078955}}
+
</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=2vgd ConSurf].
-
==About this Structure==
+
<div style="clear:both"></div>
-
2VGD is a [[Single protein]] 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=2VGD OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
-
Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases., Vardakou M, Dumon C, Murray JW, Christakopoulos P, Weiner DP, Juge N, Lewis RJ, Gilbert HJ, Flint JE, J Mol Biol. 2008 Feb 1;375(5):1293-305. Epub 2007 Nov 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18078955 18078955]
+
-
[[Category: Endo-1,4-beta-xylanase]]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Christakopoulos, P.]]
+
[[Category: Christakopoulos P]]
-
[[Category: Dumon, C.]]
+
[[Category: Dumon C]]
-
[[Category: Flint, J E.]]
+
[[Category: Flint JE]]
-
[[Category: Gilbert, H J.]]
+
[[Category: Gilbert HJ]]
-
[[Category: Juge, N.]]
+
[[Category: Juge N]]
-
[[Category: Lewis, R J.]]
+
[[Category: Lewis RJ]]
-
[[Category: Murray, J W.]]
+
[[Category: Murray JW]]
-
[[Category: Vardakou, M.]]
+
[[Category: Vardakou M]]
-
[[Category: Weiner, D P.]]
+
[[Category: Weiner DP]]
-
[[Category: Beta jelly roll]]
+
-
[[Category: Glycoside hydrolase]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Xylanase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:10:11 2008''
+

Current revision

Crystal structure of environmental isolated GH11 in complex with xylobiose and feruloyl-arabino-xylotriose

PDB ID 2vgd

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/2vgd"
Personal tools