3g53

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:59, 6 September 2023) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
'''Unreleased structure'''
 
-
The entry 3g53 is ON HOLD until Paper Publication
+
==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropropyl benzene bound to the XE4 cavity==
 +
<StructureSection load='3g53' size='340' side='right'caption='[[3g53]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3g53]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anadara_inaequivalvis Anadara inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G53 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G53 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]] 1.64&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LT1:(3-CHLOROPROPYL)BENZENE'>LT1</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=3g53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g53 OCA], [https://pdbe.org/3g53 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g53 RCSB], [https://www.ebi.ac.uk/pdbsum/3g53 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g53 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GLB1_ANAIN GLB1_ANAIN]
 +
== 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/g5/3g53_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=3g53 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.
-
Authors: Knapp, J.E., Pahl, R., Cohen, J., Nichols, J.C., Schulten, K., Gibson, Q.H., Srajer, V., Royer Jr., W.E.
+
Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.,Knapp JE, Pahl R, Cohen J, Nichols JC, Schulten K, Gibson QH, Srajer V, Royer WE Jr Structure. 2009 Nov 11;17(11):1494-504. PMID:19913484<ref>PMID:19913484</ref>
-
Description: Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropropyl benzene bound to the XE4 cavity
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3g53" style="background-color:#fffaf0;"></div>
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 15 09:52:01 2009''
+
==See Also==
 +
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Anadara inaequivalvis]]
 +
[[Category: Large Structures]]
 +
[[Category: Cohen J]]
 +
[[Category: Gibson QH]]
 +
[[Category: Knapp JE]]
 +
[[Category: Nichols JC]]
 +
[[Category: Pahl R]]
 +
[[Category: Royer Jr WE]]
 +
[[Category: Schulten K]]
 +
[[Category: Srajer V]]

Current revision

Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropropyl benzene bound to the XE4 cavity

PDB ID 3g53

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/3g53"
Personal tools