3ltd: Difference between revisions

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<StructureSection load='3ltd' size='340' side='right'caption='[[3ltd]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='3ltd' size='340' side='right'caption='[[3ltd]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ltd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LTD FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ltd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LTD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3lt8|3lt8]], [[3lt9|3lt9]], [[3lta|3lta]], [[3ltb|3ltb]], [[3ltc|3ltc]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3ltd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ltd OCA], [https://pdbe.org/3ltd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ltd RCSB], [https://www.ebi.ac.uk/pdbsum/3ltd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ltd ProSAT]</span></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=3ltd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ltd OCA], [https://pdbe.org/3ltd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ltd RCSB], [https://www.ebi.ac.uk/pdbsum/3ltd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ltd ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The creation of synthetic enzymes with predefined functions represents a major challenge in future synthetic biology applications. Here, we describe six structures of de novo proteins that have been determined using protein crystallography to address how simple enzymes perform catalysis. Three structures are of a protein, DX, selected for its stability and ability to tightly bind ATP. Despite the addition of ATP to the crystallization conditions, the presence of a bound but distorted ATP was found only under excess ATP conditions, with ADP being present under equimolar conditions or when crystallized for a prolonged period of time. A bound ADP cofactor was evident when Asp was substituted for Val at residue 65, but ATP in a linear configuration is present when Phe was substituted for Tyr at residue 43. These new structures complement previously determined structures of DX and the protein with the Phe 43 to Tyr substitution [Simmons, C. R., et al. (2009) ACS Chem. Biol. 4, 649-658] and together demonstrate the multiple ADP/ATP binding modes from which a model emerges in which the DX protein binds ATP in a configuration that represents a transitional state for the catalysis of ATP to ADP through a slow, metal-free reaction capable of multiple turnovers. This unusual observation suggests that design-free methods can be used to generate novel protein scaffolds that are tailor-made for catalysis.
Three-Dimensional Structures Reveal Multiple ADP/ATP Binding Modes for a Synthetic Class of Artificial Proteins .,Simmons CR, Magee CL, Smith DA, Lauman L, Chaput JC, Allen JP Biochemistry. 2010 Sep 16. PMID:20822107<ref>PMID:20822107</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ltd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Synthetic construct sequences]]
[[Category: Synthetic construct]]
[[Category: Allen, J P]]
[[Category: Allen JP]]
[[Category: Chaput, J C]]
[[Category: Chaput JC]]
[[Category: Magee, C L]]
[[Category: Magee CL]]
[[Category: Simmons, C R]]
[[Category: Simmons CR]]
[[Category: Alpha/beta fold]]
[[Category: Bent atp]]
[[Category: De novo protein]]
[[Category: Non-biological protein]]

Latest revision as of 13:22, 21 February 2024

X-ray structure of a non-biological ATP binding protein determined at 2.8 A by multi-wavelength anomalous dispersionX-ray structure of a non-biological ATP binding protein determined at 2.8 A by multi-wavelength anomalous dispersion

Structural highlights

3ltd is a 1 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

3ltd, resolution 2.80Å

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