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.


1dbu

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:49, 20 March 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1dbu.png|left|200px]]
 
-
<!--
+
==Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)==
-
The line below this paragraph, containing "STRUCTURE_1dbu", creates the "Structure Box" on the page.
+
<StructureSection load='1dbu' size='340' side='right'caption='[[1dbu]], [[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'>[[1dbu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBU 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=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
{{STRUCTURE_1dbu| PDB=1dbu | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbu OCA], [https://pdbe.org/1dbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbu RCSB], [https://www.ebi.ac.uk/pdbsum/1dbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbu ProSAT]</span></td></tr>
-
 
+
</table>
-
===Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)===
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/YBAK_HAEIN YBAK_HAEIN] Functions in trans to edit the amino acid from incorrectly charged Cys-tRNA(Pro) via a Cys-tRNA(Pro) deacylase activity. Probably compensates for the lack of Cys-tRNA(Pro) editing by ProRS. Is also able to deacylate Cys-tRNA(Cys), and displays weak deacylase activity in vitro against Gly-tRNA(Gly), as well as, at higher concentrations, some other correctly charged tRNAs. Does not cleave Pro-tRNA(Pro).<ref>PMID:15322138</ref> <ref>PMID:15886196</ref> <ref>PMID:21768119</ref>
-
 
+
== Evolutionary Conservation ==
-
<!--
+
[[Image:Consurf_key_small.gif|200px|right]]
-
The line below this paragraph, {{ABSTRACT_PUBMED_10813833}}, adds the Publication Abstract to the page
+
Check<jmol>
-
(as it appears on PubMed at http://www.pubmed.gov), where 10813833 is the PubMed ID number.
+
<jmolCheckbox>
-
-->
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/1dbu_consurf.spt"</scriptWhenChecked>
-
{{ABSTRACT_PUBMED_10813833}}
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1DBU is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBU OCA].
+
</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=1dbu ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
== References ==
-
<ref group="xtra">PMID:10813833</ref><references group="xtra"/>
+
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
-
[[Category: Herzberg, O.]]
+
[[Category: Large Structures]]
-
[[Category: Huang, K.]]
+
[[Category: Herzberg O]]
-
[[Category: Li, Z.]]
+
[[Category: Huang K]]
-
[[Category: S2F, Structure 2.Function Project.]]
+
[[Category: Li Z]]
-
[[Category: Zhang, H.]]
+
[[Category: Zhang H]]
-
[[Category: S2f]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Structure 2 function project]]
+
-
[[Category: Ybak]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:14:47 2009''
+

Current revision

Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)

PDB ID 1dbu

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/1dbu"
Personal tools