3l5k: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 1: Line 1:


==The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)==
==The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)==
<StructureSection load='3l5k' size='340' side='right' caption='[[3l5k]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3l5k' size='340' side='right'caption='[[3l5k]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3l5k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L5K FirstGlance]. <br>
<table><tr><td colspan='2'>[[3l5k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L5K FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2pib|2pib]], [[3hlt|3hlt]], [[3k1z|3k1z]], [[2w4m|2w4m]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HDHD1A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3l5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l5k OCA], [https://pdbe.org/3l5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l5k RCSB], [https://www.ebi.ac.uk/pdbsum/3l5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l5k ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3l5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l5k OCA], [http://pdbe.org/3l5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l5k RCSB], [http://www.ebi.ac.uk/pdbsum/3l5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l5k ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/HDHD1_HUMAN HDHD1_HUMAN]] Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine.<ref>PMID:20722631</ref>
[https://www.uniprot.org/uniprot/HDHD1_HUMAN HDHD1_HUMAN] Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine.<ref>PMID:20722631</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l5/3l5k_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l5/3l5k_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 25: Line 24:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Allerston, C]]
[[Category: Large Structures]]
[[Category: Arrowsmith, C H]]
[[Category: Allerston C]]
[[Category: Bountra, C]]
[[Category: Arrowsmith CH]]
[[Category: Delft, F von]]
[[Category: Bountra C]]
[[Category: Edwards, A]]
[[Category: Edwards A]]
[[Category: Guo, K]]
[[Category: Guo K]]
[[Category: Kavanagh, K L]]
[[Category: Kavanagh KL]]
[[Category: Muniz, J]]
[[Category: Muniz J]]
[[Category: Oppermann, U]]
[[Category: Oppermann U]]
[[Category: Picaud, S]]
[[Category: Picaud S]]
[[Category: Structural genomic]]
[[Category: Ugochukwu E]]
[[Category: Ugochukwu, E]]
[[Category: Weigelt J]]
[[Category: Weigelt, J]]
[[Category: Yue WW]]
[[Category: Yue, W W]]
[[Category: Von Delft F]]
[[Category: Haloacid dehalogenase-like hydrolase domain containing 1a]]
[[Category: Hdhd1a]]
[[Category: Hydrolase]]
[[Category: Polymorphism]]
[[Category: Sgc]]

Latest revision as of 11:31, 6 September 2023

The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)

Structural highlights

3l5k is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HDHD1_HUMAN Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Preumont A, Rzem R, Vertommen D, Van Schaftingen E. HDHD1, which is often deleted in X-linked ichthyosis, encodes a pseudouridine-5'-phosphatase. Biochem J. 2010 Oct 15;431(2):237-44. doi: 10.1042/BJ20100174. PMID:20722631 doi:http://dx.doi.org/10.1042/BJ20100174

3l5k, resolution 2.00Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3l5k&oldid=3866303"