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.


3ekm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
==Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP==
==Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP==
-
<StructureSection load='3ekm' size='340' side='right' caption='[[3ekm]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+
<StructureSection load='3ekm' size='340' side='right'caption='[[3ekm]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3ekm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EKM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3ekm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EKM FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDR:(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC+ACID'>ZDR</scene></td></tr>
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZDR:(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC+ACID'>ZDR</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ejx|3ejx]]</td></tr>
+
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ejx|3ejx]]</div></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </span></td></tr>
+
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </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=3ekm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ekm OCA], [http://pdbe.org/3ekm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ekm RCSB], [http://www.ebi.ac.uk/pdbsum/3ekm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ekm ProSAT]</span></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=3ekm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ekm OCA], [https://pdbe.org/3ekm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ekm RCSB], [https://www.ebi.ac.uk/pdbsum/3ekm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ekm ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/DAPF_ARATH DAPF_ARATH]] Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.<ref>PMID:15652176</ref>
+
[[https://www.uniprot.org/uniprot/DAPF_ARATH DAPF_ARATH]] Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.<ref>PMID:15652176</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 37: Line 37:
[[Category: Arath]]
[[Category: Arath]]
[[Category: Diaminopimelate epimerase]]
[[Category: Diaminopimelate epimerase]]
 +
[[Category: Large Structures]]
[[Category: Belkum, M J.van]]
[[Category: Belkum, M J.van]]
[[Category: Cherney, M M]]
[[Category: Cherney, M M]]

Revision as of 11:52, 16 February 2022

Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP

PDB ID 3ekm

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/3ekm"
Personal tools