2h9j

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2h9j" size="450" color="white" frame="true" align="right" spinBox="true" caption="2h9j, resolution 1.75&Aring;" /> '''Structure of Hen egg...)
Current revision (01:00, 21 November 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2h9j.gif|left|200px]]<br /><applet load="2h9j" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2h9j, resolution 1.75&Aring;" />
 
-
'''Structure of Hen egg white lysozyme soaked with Ni2-Xylylbicyclam'''<br />
 
-
==Overview==
+
==Structure of Hen egg white lysozyme soaked with Ni2-Xylylbicyclam==
-
Nickel(II)-xylylbicyclam is a potent anti-HIV agent and binds strongly to, the CXCR4 co-receptor. We have investigated configurational equilibria of, Ni(II)-cyclam derivatives, since these are important for receptor, recognition. Crystallographic studies show that both trans and cis, configurations are readily formed: [Ni(cyclam)(OAc)(2)] x H(2)O adopts the, trans-III configuration with axial monodentate acetates, as does, [Ni(benzylcyclam)(NO(3))(2)] with axial nitrate ligands, whereas, [Ni(benzylcyclam)(OAc)](OAc)2 x H(2)O has an unusual folded cis-V, configuration with Ni(II) coordination to bidentate acetate. UV/Vis and, NMR studies show that the octahedral trans-III configuration slowly, converts to square-planar trans-I in aqueous solution. For, Ni(II)-xylylbicyclam, a mixture of cis-V and trans-I configurations was, detected in solution. X-ray diffraction studies showed that crystals of, lysozyme soaked in Ni(II)-cyclam or Ni(II) (2)-xylylbicyclam contain two, major binding sites, one involving Ni(II) coordination to Asp101 and, hydrophobic interactions between the cyclam ring and Trp62 and Trp63, and, the second hydrophobic interactions with Trp123. For Ni(II)-cyclam bound, to Asp101, the cis-V configuration predominates.
+
<StructureSection load='2h9j' size='340' side='right'caption='[[2h9j]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2h9j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9J 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]] 1.75&#8491;</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>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=2h9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9j OCA], [https://pdbe.org/2h9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9j RCSB], [https://www.ebi.ac.uk/pdbsum/2h9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9j ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
 +
== 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/h9/2h9j_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2h9j ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Nickel(II)-xylylbicyclam is a potent anti-HIV agent and binds strongly to the CXCR4 co-receptor. We have investigated configurational equilibria of Ni(II)-cyclam derivatives, since these are important for receptor recognition. Crystallographic studies show that both trans and cis configurations are readily formed: [Ni(cyclam)(OAc)(2)] x H(2)O adopts the trans-III configuration with axial monodentate acetates, as does [Ni(benzylcyclam)(NO(3))(2)] with axial nitrate ligands, whereas [Ni(benzylcyclam)(OAc)](OAc)2 x H(2)O has an unusual folded cis-V configuration with Ni(II) coordination to bidentate acetate. UV/Vis and NMR studies show that the octahedral trans-III configuration slowly converts to square-planar trans-I in aqueous solution. For Ni(II)-xylylbicyclam, a mixture of cis-V and trans-I configurations was detected in solution. X-ray diffraction studies showed that crystals of lysozyme soaked in Ni(II)-cyclam or Ni(II) (2)-xylylbicyclam contain two major binding sites, one involving Ni(II) coordination to Asp101 and hydrophobic interactions between the cyclam ring and Trp62 and Trp63, and the second hydrophobic interactions with Trp123. For Ni(II)-cyclam bound to Asp101, the cis-V configuration predominates.
-
==About this Structure==
+
Configurations of nickel-cyclam antiviral complexes and protein recognition.,Hunter TM, McNae IW, Simpson DP, Smith AM, Moggach S, White F, Walkinshaw MD, Parsons S, Sadler PJ Chemistry. 2007;13(1):40-50. PMID:17120266<ref>PMID:17120266</ref>
-
2H9J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with CL, NA, NI and MM5 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2H9J OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Configurations of nickel-cyclam antiviral complexes and protein recognition., Hunter TM, McNae IW, Simpson DP, Smith AM, Moggach S, White F, Walkinshaw MD, Parsons S, Sadler PJ, Chemistry. 2007;13(1):40-50. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17120266 17120266]
+
</div>
-
[[Category: Gallus gallus]]
+
<div class="pdbe-citations 2h9j" style="background-color:#fffaf0;"></div>
-
[[Category: Lysozyme]]
+
-
[[Category: Single protein]]
+
-
[[Category: Hunter, T.M.]]
+
-
[[Category: McNae, I.W.]]
+
-
[[Category: Sadler, P.J.]]
+
-
[[Category: Walkinshaw, M.D.]]
+
-
[[Category: CL]]
+
-
[[Category: MM5]]
+
-
[[Category: NA]]
+
-
[[Category: NI]]
+
-
[[Category: cyclam]]
+
-
[[Category: lysozyme]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:37:23 2007''
+
==See Also==
 +
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Gallus gallus]]
 +
[[Category: Large Structures]]
 +
[[Category: Hunter TM]]
 +
[[Category: McNae IW]]
 +
[[Category: Sadler PJ]]
 +
[[Category: Walkinshaw MD]]

Current revision

Structure of Hen egg white lysozyme soaked with Ni2-Xylylbicyclam

PDB ID 2h9j

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/2h9j"
Personal tools