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.


3daf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:43, 30 August 2023) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII cocrystallized with cyanide==
==The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII cocrystallized with cyanide==
-
<StructureSection load='3daf' size='340' side='right' caption='[[3daf]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+
<StructureSection load='3daf' size='340' side='right'caption='[[3daf]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3daf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DAF FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3daf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DAF 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=CYN:CYANIDE+ION'>CYN</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]], [[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=CYN:CYANIDE+ION'>CYN</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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 ATCC 43067])</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=3daf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daf OCA], [https://pdbe.org/3daf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3daf RCSB], [https://www.ebi.ac.uk/pdbsum/3daf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3daf 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=3daf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daf OCA], [http://pdbe.org/3daf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3daf RCSB], [http://www.ebi.ac.uk/pdbsum/3daf 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/3daf_consurf.spt"</scriptWhenChecked>
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/3daf_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>
Line 34: Line 33:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]
+
[[Category: Large Structures]]
-
[[Category: Atcc 43067]]
+
[[Category: Methanocaldococcus jannaschii]]
-
[[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 cocrystallized with cyanide

PDB ID 3daf

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/3daf"
Personal tools