This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5c9f

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:19, 6 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii==
==Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii==
-
<StructureSection load='5c9f' size='340' side='right' caption='[[5c9f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+
<StructureSection load='5c9f' size='340' side='right'caption='[[5c9f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<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>
+
<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>
-
</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>
+
</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>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5c9b|5c9b]], [[5c9d|5c9d]]</td></tr>
+
<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>
-
<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>
+
<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>
-
<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>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q92FY8_RICCN Q92FY8_RICCN]
-
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.
+
-
 
+
-
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>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5c9f" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc vr-613]]
+
[[Category: Large Structures]]
-
[[Category: Cruz, R]]
+
[[Category: Rickettsia conorii]]
-
[[Category: Curto, P]]
+
[[Category: Cruz R]]
-
[[Category: Faro, C]]
+
[[Category: Curto P]]
-
[[Category: Gustchina, A]]
+
[[Category: Faro C]]
-
[[Category: Li, M]]
+
[[Category: Gustchina A]]
-
[[Category: Martinez, J]]
+
[[Category: Li M]]
-
[[Category: Simoes, I]]
+
[[Category: Martinez J]]
-
[[Category: Simoes, M]]
+
[[Category: Simoes I]]
-
[[Category: Wlodawer, A]]
+
[[Category: Simoes M]]
-
[[Category: Aprick]]
+
[[Category: Wlodawer A]]
-
[[Category: Hydrolase]]
+
-
[[Category: Pepsin]]
+

Current revision

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

PDB ID 5c9f

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5c9f"
Personal tools