3v1d: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
Line 3: Line 3:
<StructureSection load='3v1d' size='340' side='right'caption='[[3v1d]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
<StructureSection load='3v1d' size='340' side='right'caption='[[3v1d]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3v1d]] is a 8 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=3V1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1D FirstGlance]. <br>
<table><tr><td colspan='2'>[[3v1d]] is a 8 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=3V1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1D FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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]] 1.239&#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;'>[[1yzm|1yzm]], [[3v1a|3v1a]], [[3v1b|3v1b]], [[3v1c|3v1c]], [[3v1e|3v1e]], [[3v1f|3v1f]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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=3v1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1d OCA], [https://pdbe.org/3v1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1d RCSB], [https://www.ebi.ac.uk/pdbsum/3v1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1d 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=3v1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1d OCA], [https://pdbe.org/3v1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1d RCSB], [https://www.ebi.ac.uk/pdbsum/3v1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1d ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Computationally designing protein-protein interactions with high affinity and desired orientation is a challenging task. Incorporating metal-binding sites at the target interface may be one approach for increasing affinity and specifying the binding mode, thereby improving robustness of designed interactions for use as tools in basic research as well as in applications from biotechnology to medicine. Here we describe a Rosetta-based approach for the rational design of a protein monomer to form a zinc-mediated, symmetric homodimer. Our metal interface design, named MID1 (NESG target ID OR37), forms a tight dimer in the presence of zinc (MID1-zinc) with a dissociation constant &lt;30 nM. Without zinc the dissociation constant is 4 muM. The crystal structure of MID1-zinc shows good overall agreement with the computational model, but only three out of four designed histidines coordinate zinc. However, a histidine-to-glutamate point mutation resulted in four-coordination of zinc, and the resulting metal binding site and dimer orientation closely matches the computational model (Calpha rmsd = 1.4 A).
Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer.,Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B J Am Chem Soc. 2011 Dec 15. PMID:22092237<ref>PMID:22092237</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3v1d" 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: Der, B S]]
[[Category: Der BS]]
[[Category: Kuhlman, B]]
[[Category: Kuhlman B]]
[[Category: Machius, M]]
[[Category: Machius M]]
[[Category: Miley, M J]]
[[Category: Miley MJ]]
[[Category: De novo protein]]
[[Category: Helix-turn-helix]]
[[Category: Metal binding protein]]
[[Category: Zinc homodimerization]]

Latest revision as of 14:14, 14 March 2024

Crystal structure of de novo designed MID1-cobalt

3v1d, resolution 1.24Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=3v1d&oldid=4099273"