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.


3dag

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:43, 30 August 2023) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII==
==The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII==
-
<StructureSection load='3dag' size='340' side='right' caption='[[3dag]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+
<StructureSection load='3dag' size='340' side='right'caption='[[3dag]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3dag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. The March 2009 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Hydrogenase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_3 10.2210/rcsb_pdb/mom_2009_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DAG FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3dag]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. The March 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Hydrogenase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_3 10.2210/rcsb_pdb/mom_2009_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DAG FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FEG:5-O-[(S)-{[2-(CARBOXYMETHYL)-6-HYDROXY-3,5-DIMETHYLPYRIDIN-4-YL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE'>FEG</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]] 1.75&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2boj|2boj]], [[3daf|3daf]], [[3f46|3f46]], [[3f47|3f47]]</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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FEG:5-O-[(S)-{[2-(CARBOXYMETHYL)-6-HYDROXY-3,5-DIMETHYLPYRIDIN-4-YL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE'>FEG</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hmd, MJ0784 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3dag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dag OCA], [https://pdbe.org/3dag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dag RCSB], [https://www.ebi.ac.uk/pdbsum/3dag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dag ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5,10-methenyltetrahydromethanopterin_hydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.2 1.12.98.2] </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=3dag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dag OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dag RCSB], [http://www.ebi.ac.uk/pdbsum/3dag PDBsum]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/HMD_METJA HMD_METJA]] Catalyzes the reversible reduction of methenyl-H(4)MPT(+) to methylene-H(4)MPT (By similarity).
+
[https://www.uniprot.org/uniprot/HMD_METJA HMD_METJA] Catalyzes the reversible reduction of methenyl-H(4)MPT(+) to methylene-H(4)MPT (By similarity).
== 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/da/3dag_consurf.spt"</scriptWhenChecked>
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/3dag_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=3dag ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
Line 29: 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 3dag" style="background-color:#fffaf0;"></div>
-
==See Also==
+
-
*[[Teaching Scenes%2C Tutorials%2C and Educators' Pages|Teaching Scenes%2C Tutorials%2C and Educators' Pages]]
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]
 
[[Category: Hydrogenase]]
[[Category: Hydrogenase]]
 +
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
-
[[Category: Ermler, U]]
+
[[Category: Ermler U]]
-
[[Category: Pilak, O]]
+
[[Category: Pilak O]]
-
[[Category: Shima, S]]
+
[[Category: Shima S]]
-
[[Category: Thauer, R K]]
+
[[Category: Thauer RK]]
-
[[Category: Warkentin, E]]
+
[[Category: Warkentin E]]
-
[[Category: Helix bundle]]
+
-
[[Category: Methanogenesis]]
+
-
[[Category: One-carbon metabolism]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Rossmann fold]]
+

Current revision

The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII

PDB ID 3dag

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/3dag"
Personal tools