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.


1dzk

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:56, 20 March 2024) (edit) (undo)
 
(20 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dzk.gif|left|200px]]<br />
 
-
<applet load="1dzk" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1dzk, resolution 1.48&Aring;" />
 
-
'''PORCINE ODORANT BINDING PROTEIN COMPLEXED WITH PYRAZINE (2-ISOBUTYL-3-METOXYPYRAZINE)'''<br />
 
-
==Overview==
+
==Porcine Odorant Binding Protein Complexed with pyrazine (2-isobutyl-3-metoxypyrazine)==
-
Porcine odorant binding protein (pOBP) is a monomer of 157 amino acid, residues, purified in abundance from pig nasal mucosa. In contrast to the, observation on lipocalins as retinol binding protein (RBP), major urinary, protein (MUP) or bovine odorant binding protein (bOBP), no naturally, occurring ligand was found in the beta-barrel cavity of pOBP. Porcine OBP, was therefore chosen as a simple model for structure/function studies with, odorant molecules. In competition experiments with tritiated pyrazine, the, affinity of pOBP towards several odorant molecules belonging to different, chemical classes has been found to be of the micromolar order, with a 1:1, stoichiometry. The X-ray structures of pOBP complexed to these molecules, were determined at resolution between 2.15 and 1.4 A. As expected, the, electron density of the odorant molecules was observed into the, hydrophobic beta-barrel of the lipocalin. Inside this cavity, very few, specific interactions were established between the odorant molecule and, the amino acid side-chains, which did not undergo significant, conformational change. The high B-factors observed for the odorant, molecules as well as the existence of alternative conformations reveal a, non-specific mode of binding of the odorant molecules in the cavity.
+
<StructureSection load='1dzk' size='340' side='right'caption='[[1dzk]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1dzk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DZK FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.48&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PRZ:2-ISOBUTYL-3-METHOXYPYRAZINE'>PRZ</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=1dzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dzk OCA], [https://pdbe.org/1dzk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dzk RCSB], [https://www.ebi.ac.uk/pdbsum/1dzk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dzk ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/OBP_PIG OBP_PIG] This protein is found in nasal epithelium and it binds a wide variety of chemical odorants.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dz/1dzk_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dzk ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1DZK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with PRZ as [http://en.wikipedia.org/wiki/ligand ligand]. Structure known Active Sites: AC1 and AC2. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DZK OCA].
+
*[[Odorant binding protein 3D structures|Odorant binding protein 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Complexes of porcine odorant binding protein with odorant molecules belonging to different chemical classes., Vincent F, Spinelli S, Ramoni R, Grolli S, Pelosi P, Cambillau C, Tegoni M, J Mol Biol. 2000 Jun 30;300(1):127-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10864504 10864504]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Sus scrofa]]
[[Category: Sus scrofa]]
-
[[Category: Cambillau, C.]]
+
[[Category: Cambillau C]]
-
[[Category: Spinelli, S.]]
+
[[Category: Spinelli S]]
-
[[Category: Tegoni, M.]]
+
[[Category: Tegoni M]]
-
[[Category: Vincent, F.]]
+
[[Category: Vincent F]]
-
[[Category: PRZ]]
+
-
[[Category: lipocalins]]
+
-
[[Category: odorant binding protein]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 16:03:02 2007''
+

Current revision

Porcine Odorant Binding Protein Complexed with pyrazine (2-isobutyl-3-metoxypyrazine)

PDB ID 1dzk

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/1dzk"
Personal tools