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.


3g4v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:59, 6 September 2023) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropentane bound to the XE4 cavity==
==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropentane bound to the XE4 cavity==
-
<StructureSection load='3g4v' size='340' side='right' caption='[[3g4v]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+
<StructureSection load='3g4v' size='340' side='right'caption='[[3g4v]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3g4v]] is a 2 chain structure 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=3G4V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G4V FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3g4v]] 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=3G4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G4V FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7CL:1-CHLOROPENTANE'>7CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4sdh|4sdh]], [[3sdh|3sdh]], [[3g4q|3g4q]], [[3g4r|3g4r]], [[3g4u|3g4u]], [[3g46|3g46]], [[3g4w|3g4w]], [[3g4y|3g4y]], [[3g52|3g52]], [[3g53|3g53]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7CL:1-CHLOROPENTANE'>7CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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 Scapharca inaequivalvis])</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=3g4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4v OCA], [https://pdbe.org/3g4v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g4v RCSB], [https://www.ebi.ac.uk/pdbsum/3g4v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g4v ProSAT]</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=3g4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g4v RCSB], [http://www.ebi.ac.uk/pdbsum/3g4v PDBsum]</span></td></tr>
+
</table>
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GLB1_ANAIN GLB1_ANAIN]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
-
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g4v_consurf.spt"</scriptWhenChecked>
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g4v_consurf.spt"</scriptWhenChecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
+
</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=3g4v ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
Line 26: Line 28:
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
 +
<div class="pdbe-citations 3g4v" style="background-color:#fffaf0;"></div>
==See Also==
==See Also==
Line 33: Line 36:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Scapharca inaequivalvis]]
+
[[Category: Anadara inaequivalvis]]
-
[[Category: Cohen, J]]
+
[[Category: Large Structures]]
-
[[Category: Gibson, Q H]]
+
[[Category: Cohen J]]
-
[[Category: Knapp, J E]]
+
[[Category: Gibson QH]]
-
[[Category: Nichols, J C]]
+
[[Category: Knapp JE]]
-
[[Category: Pahl, R]]
+
[[Category: Nichols JC]]
-
[[Category: Royer, W E]]
+
[[Category: Pahl R]]
-
[[Category: Schulten, K]]
+
[[Category: Royer Jr WE]]
-
[[Category: Srajer, V]]
+
[[Category: Schulten K]]
-
[[Category: Allostery]]
+
[[Category: Srajer V]]
-
[[Category: Heme]]
+
-
[[Category: Iron]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Oxygen affinity]]
+
-
[[Category: Oxygen binding]]
+
-
[[Category: Oxygen storage/transport]]
+
-
[[Category: Oxygen transport]]
+

Current revision

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

PDB ID 3g4v

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/3g4v"
Personal tools