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3g46

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Revision as of 07:54, 5 December 2018

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

Structural highlights

3g46 is a 2 chain structure with sequence from Anain. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	3sdh, 4sdh, 3g4q, 3g4r, 3g4u, 3g4v, 3g4w, 3g4y, 3g52, 3g53
Gene:	HBI (ANAIN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Knapp JE, Pahl R, Cohen J, Nichols JC, Schulten K, Gibson QH, Srajer V, Royer WE Jr. Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis. Structure. 2009 Nov 11;17(11):1494-504. PMID:19913484 doi:10.1016/j.str.2009.09.004

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3g46"

@@ Line 1: / Line 1: @@
 ==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloroform bound to the XE4 cavity==
 <StructureSection load='3g46' size='340' side='right' caption='[[3g46]], [[Resolution|resolution]] 0.91&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3sdh|3sdh]], [[4sdh|4sdh]], [[3g4q|3g4q]], [[3g4r|3g4r]], [[3g4u|3g4u]], [[3g4v|3g4v]], [[3g4w|3g4w]], [[3g4y|3g4y]], [[3g52|3g52]], [[3g53|3g53]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 ANAIN])</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=3g46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g46 OCA], [http://pdbe.org/3g46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g46 RCSB], [http://www.ebi.ac.uk/pdbsum/3g46 PDBsum]</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=3g46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g46 OCA], [http://pdbe.org/3g46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g46 RCSB], [http://www.ebi.ac.uk/pdbsum/3g46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g46 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g46_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g46_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 44: / Line 45: @@
 [[Category: Srajer, V]]
 [[Category: Allostery]]
+[[Category: Cytoplasm]]
 [[Category: Heme]]
 [[Category: Iron]]

3g46

From Proteopedia

Revision as of 07:54, 5 December 2018

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

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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