5c9f

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==Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii==
==Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii==
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<StructureSection load='5c9f' size='340' side='right' caption='[[5c9f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='5c9f' size='340' side='right'caption='[[5c9f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5c9f]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_vr-613 Atcc vr-613]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C9F FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5c9f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rickettsia_conorii Rickettsia conorii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C9F FirstGlance]. <br>
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</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=NA:SODIUM+ION'>NA</scene></td></tr>
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</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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5c9b|5c9b]], [[5c9d|5c9d]]</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=NA:SODIUM+ION'>NA</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RC1339 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=781 ATCC VR-613])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5c9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9f OCA], [https://pdbe.org/5c9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c9f RCSB], [https://www.ebi.ac.uk/pdbsum/5c9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9f ProSAT]</span></td></tr>
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<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=5c9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9f OCA], [http://pdbe.org/5c9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c9f RCSB], [http://www.ebi.ac.uk/pdbsum/5c9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9f ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q92FY8_RICCN Q92FY8_RICCN]
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The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at a resolution of 1.8 A. The decamer adopts a novel double-folded structure in which the direction of progression of the backbone changes at the two thymine residues. Intra-strand stacking interactions (including an interaction between the endocylic O atom of a ribose moiety and the adjacent purine base), hydrogen bonds and cobalt-ion interactions stabilize the double-folded structure of the single strand. Two such double-folded strands come together in the crystal to form a dimer. Inter-strand Watson-Crick hydrogen bonds form four base pairs. This portion of the decamer structure is similar to that observed in other previously reported oligonucleotide structures and has been dubbed a `bi-loop'. Both the double-folded single-strand structure, as well as the dimeric bi-loop structure, serve as starting points to construct models for triplet-repeat DNA sequences, which have been implicated in many human diseases.
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The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences.,Thirugnanasambandam A, Karthik S, Mandal PK, Gautham N Acta Crystallogr D Biol Crystallogr. 2015 Oct;71(Pt 10):2119-26. doi:, 10.1107/S1399004715013930. Epub 2015 Sep 30. PMID:26457435<ref>PMID:26457435</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5c9f" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc vr-613]]
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[[Category: Large Structures]]
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[[Category: Cruz, R]]
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[[Category: Rickettsia conorii]]
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[[Category: Curto, P]]
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[[Category: Cruz R]]
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[[Category: Faro, C]]
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[[Category: Curto P]]
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[[Category: Gustchina, A]]
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[[Category: Faro C]]
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[[Category: Li, M]]
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[[Category: Gustchina A]]
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[[Category: Martinez, J]]
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[[Category: Li M]]
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[[Category: Simoes, I]]
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[[Category: Martinez J]]
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[[Category: Simoes, M]]
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[[Category: Simoes I]]
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[[Category: Wlodawer, A]]
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[[Category: Simoes M]]
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[[Category: Aprick]]
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[[Category: Wlodawer A]]
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[[Category: Hydrolase]]
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[[Category: Pepsin]]
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Current revision

Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii

PDB ID 5c9f

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