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.


3vmm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
==Crystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis==
==Crystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis==
-
<StructureSection load='3vmm' size='340' side='right' caption='[[3vmm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+
<StructureSection load='3vmm' size='340' side='right'caption='[[3vmm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3vmm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VMM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3vmm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VMM FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P0D:(2S)-3-[(S)-[(1R)-1-AMINOETHYL](PHOSPHONOOXY)PHOSPHORYL]-2-BENZYLPROPANOIC+ACID'>P0D</scene></td></tr>
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P0D:(2S)-3-[(S)-[(1R)-1-AMINOETHYL](PHOSPHONOOXY)PHOSPHORYL]-2-BENZYLPROPANOIC+ACID'>P0D</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bacD, BSU37710, ipa-83d ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
+
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bacD, BSU37710, ipa-83d ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-amino-acid_alpha-ligase L-amino-acid alpha-ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.28 6.3.2.28] </span></td></tr>
+
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-amino-acid_alpha-ligase L-amino-acid alpha-ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.28 6.3.2.28] </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=3vmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vmm OCA], [http://pdbe.org/3vmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vmm RCSB], [http://www.ebi.ac.uk/pdbsum/3vmm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vmm 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=3vmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vmm OCA], [https://pdbe.org/3vmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vmm RCSB], [https://www.ebi.ac.uk/pdbsum/3vmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vmm ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/BACD_BACSU BACD_BACSU]] Catalyzes the formation of alpha-dipeptides from various L-amino acids in the presence of ATP. Has a broad substrate specificity. Does not accept lysine, arginine, glutamate, aspartate and proline as a substrate. Probably catalyzes the ligation of L-alanine and L-anticapsin to produce the final bacilysin antibiotic.
+
[[https://www.uniprot.org/uniprot/BACD_BACSU BACD_BACSU]] Catalyzes the formation of alpha-dipeptides from various L-amino acids in the presence of ATP. Has a broad substrate specificity. Does not accept lysine, arginine, glutamate, aspartate and proline as a substrate. Probably catalyzes the ligation of L-alanine and L-anticapsin to produce the final bacilysin antibiotic.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 24: Line 24:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bacillus globigii migula 1900]]
+
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: L-amino-acid alpha-ligase]]
[[Category: L-amino-acid alpha-ligase]]
 +
[[Category: Large Structures]]
[[Category: Higuchi, Y]]
[[Category: Higuchi, Y]]
[[Category: Shomura, Y]]
[[Category: Shomura, Y]]

Revision as of 18:53, 27 July 2022

Crystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis

PDB ID 3vmm

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/3vmm"
Personal tools