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.


1v9p

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (00:00, 28 December 2023) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal Structure Of Nad+-Dependent DNA Ligase==
==Crystal Structure Of Nad+-Dependent DNA Ligase==
-
<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+
<StructureSection load='1v9p' size='340' side='right'caption='[[1v9p]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43280 Atcc 43280]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.9&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dgt|1dgt]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 ATCC 43280])</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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [https://pdbe.org/1v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [https://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p 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/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://pdbe.org/1v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p PDBsum]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/DNLJ_THEFI DNLJ_THEFI]] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.<ref>PMID:15268945</ref>
+
[https://www.uniprot.org/uniprot/DNLJ_THEFI DNLJ_THEFI] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.<ref>PMID:15268945</ref>
== 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/v9/1v9p_consurf.spt"</scriptWhenChecked>
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v9/1v9p_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=1v9p ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
Line 32: Line 31:
==See Also==
==See Also==
-
*[[DNA ligase|DNA ligase]]
+
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc 43280]]
+
[[Category: Large Structures]]
-
[[Category: Chang, C]]
+
[[Category: Thermus filiformis]]
-
[[Category: Kim, H K]]
+
[[Category: Chang C]]
-
[[Category: Kwon, S K]]
+
[[Category: Kim HK]]
-
[[Category: Lee, J Y]]
+
[[Category: Kwon SK]]
-
[[Category: Moon, J]]
+
[[Category: Lee JY]]
-
[[Category: Song, H K]]
+
[[Category: Moon J]]
-
[[Category: Suh, S W]]
+
[[Category: Song HK]]
-
[[Category: Yang, J K]]
+
[[Category: Suh SW]]
-
[[Category: Ligase]]
+
[[Category: Yang JK]]
-
[[Category: Nad+-dependent dna ligase]]
+

Current revision

Crystal Structure Of Nad+-Dependent DNA Ligase

PDB ID 1v9p

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/1v9p"
Personal tools