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3g4y

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[[Image:3g4y.png|left|200px]]
 
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==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloromethyl benzene bound to the XE4 cavity==
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The line below this paragraph, containing "STRUCTURE_3g4y", creates the "Structure Box" on the page.
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<StructureSection load='3g4y' size='340' side='right'caption='[[3g4y]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3g4y]] 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=3G4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G4Y FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9CL:(CHLOROMETHYL)BENZENE'>9CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
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{{STRUCTURE_3g4y| PDB=3g4y | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3g4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4y OCA], [https://pdbe.org/3g4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g4y RCSB], [https://www.ebi.ac.uk/pdbsum/3g4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4y ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GLB1_ANAIN GLB1_ANAIN]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g4y_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3g4y ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloromethyl benzene bound to the XE4 cavity===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19913484}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3g4y" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19913484 is the PubMed ID number.
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{{ABSTRACT_PUBMED_19913484}}
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==About this Structure==
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[[3g4y]] is a 2 chain structure of [[Hemoglobin]] with sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G4Y OCA].
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==See Also==
==See Also==
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*[[Hemoglobin]]
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*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:19913484</ref><references group="xtra"/>
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__TOC__
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[[Category: Scapharca inaequivalvis]]
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</StructureSection>
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[[Category: Cohen, J.]]
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[[Category: Anadara inaequivalvis]]
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[[Category: Gibson, Q H.]]
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[[Category: Large Structures]]
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[[Category: Knapp, J E.]]
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[[Category: Cohen J]]
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[[Category: Nichols, J C.]]
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[[Category: Gibson QH]]
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[[Category: Pahl, R.]]
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[[Category: Knapp JE]]
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[[Category: Royer, W E.]]
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[[Category: Nichols JC]]
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[[Category: Schulten, K.]]
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[[Category: Pahl R]]
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[[Category: Srajer, V.]]
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[[Category: Royer Jr WE]]
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[[Category: Schulten K]]
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[[Category: Srajer V]]

Current revision

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

PDB ID 3g4y

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