3k2x: Difference between revisions

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[[Image:3k2x.png|left|200px]]


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==Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with 5'-iodo-cytosine==
The line below this paragraph, containing "STRUCTURE_3k2x", creates the "Structure Box" on the page.
<StructureSection load='3k2x' size='340' side='right'caption='[[3k2x]], [[Resolution|resolution]] 1.85&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'>[[3k2x]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K2X 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]] 1.85&#8491;</td></tr>
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<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=I5A:5-DEOXY-5-IODOCYTIDINE'>I5A</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_3k2x| PDB=3k2x |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3k2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k2x OCA], [https://pdbe.org/3k2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k2x RCSB], [https://www.ebi.ac.uk/pdbsum/3k2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k2x ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ISPF_BURP1 ISPF_BURP1] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]
== 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/k2/3k2x_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=3k2x ConSurf].
<div style="clear:both"></div>


===Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with 5'-iodo-cytosine===
==See Also==
 
*[[MECDP synthase 3D structures|MECDP synthase 3D structures]]
 
__TOC__
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</StructureSection>
The line below this paragraph, {{ABSTRACT_PUBMED_21359640}}, adds the Publication Abstract to the page
[[Category: Burkholderia pseudomallei 1710b]]
(as it appears on PubMed at http://www.pubmed.gov), where 21359640 is the PubMed ID number.
[[Category: Large Structures]]
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{{ABSTRACT_PUBMED_21359640}}
 
==About this Structure==
[[3k2x]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K2X OCA].
 
==Reference==
<ref group="xtra">PMID:021359640</ref><references group="xtra"/>
[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
[[Category: Burkholderia pseudomallei]]
[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
[[Category: Fbdd]]
[[Category: Fragment crystallography]]
[[Category: Fragment-based drug design]]
[[Category: Fragments of life]]
[[Category: Isoprene biosynthesis]]
[[Category: Lyase]]
[[Category: Metal-binding]]
[[Category: Niaid]]
[[Category: Seattle structural genomics center for infectious disease]]
[[Category: Ssgcid]]

Latest revision as of 13:14, 21 February 2024

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with 5'-iodo-cytosineCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with 5'-iodo-cytosine

Structural highlights

3k2x is a 3 chain structure with sequence from Burkholderia pseudomallei 1710b. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.85Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ISPF_BURP1 Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]

Evolutionary Conservation

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

See Also

3k2x, resolution 1.85Å

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