3vb8: Difference between revisions

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<StructureSection load='3vb8' size='340' side='right'caption='[[3vb8]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<StructureSection load='3vb8' size='340' side='right'caption='[[3vb8]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3vb8]] is a 2 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=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3vb8]] is a 2 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=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [https://pdbe.org/3vb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [https://www.ebi.ac.uk/pdbsum/3vb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vb8 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=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [https://pdbe.org/3vb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [https://www.ebi.ac.uk/pdbsum/3vb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vb8 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.
Computational Design of a Protein-Based Enzyme Inhibitor.,Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, Aramini J, Kornhaber G, Hunt JF, Tong L, Montelione GT, Baker D J Mol Biol. 2013 Jul 1. pii: S0022-2836(13)00430-0. doi:, 10.1016/j.jmb.2013.06.035. PMID:23827138<ref>PMID:23827138</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3vb8" 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: Acton, T B]]
[[Category: Acton TB]]
[[Category: Baker, D]]
[[Category: Baker D]]
[[Category: Ciccosanti, C]]
[[Category: Ciccosanti C]]
[[Category: Everett, J K]]
[[Category: Everett JK]]
[[Category: Hunt, J F]]
[[Category: Hunt JF]]
[[Category: Montelione, G T]]
[[Category: Montelione GT]]
[[Category: Structural genomic]]
[[Category: Procko E]]
[[Category: Procko, E]]
[[Category: Sahdev S]]
[[Category: Sahdev, S]]
[[Category: Seetharaman J]]
[[Category: Seetharaman, J]]
[[Category: Su M]]
[[Category: Su, M]]
[[Category: Tong L]]
[[Category: Tong, L]]
[[Category: Xiao R]]
[[Category: Xiao, R]]
[[Category: De novo protein]]
[[Category: Nesg]]
[[Category: Psi-biology]]

Latest revision as of 17:22, 14 March 2024

Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43

Structural highlights

3vb8 is a 2 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 2.9Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

3vb8, resolution 2.90Å

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