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.


6dt1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:13, 11 October 2023) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate==
==Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate==
-
<StructureSection load='6dt1' size='340' side='right' caption='[[6dt1]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
+
<StructureSection load='6dt1' size='340' side='right'caption='[[6dt1]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6dt1]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DT1 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6dt1]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DT1 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.75&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </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=6dt1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dt1 OCA], [https://pdbe.org/6dt1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dt1 RCSB], [https://www.ebi.ac.uk/pdbsum/6dt1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dt1 ProSAT]</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=6dt1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dt1 OCA], [http://pdbe.org/6dt1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dt1 RCSB], [http://www.ebi.ac.uk/pdbsum/6dt1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dt1 ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/DNLI_BPT4 DNLI_BPT4]] DNA ligase, which is expressed in the early stage of lytic development, has been implicated in T4 DNA synthesis and genetic recombination. It may also play a role in T4 DNA repair.
+
[https://www.uniprot.org/uniprot/DNLI_BPT4 DNLI_BPT4] DNA ligase, which is expressed in the early stage of lytic development, has been implicated in T4 DNA synthesis and genetic recombination. It may also play a role in T4 DNA repair.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 20: Line 19:
</div>
</div>
<div class="pdbe-citations 6dt1" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 6dt1" style="background-color:#fffaf0;"></div>
 +
 +
==See Also==
 +
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Aihara, H]]
+
[[Category: Escherichia virus T4]]
-
[[Category: Shi, K]]
+
[[Category: Large Structures]]
-
[[Category: Ligase]]
+
[[Category: Aihara H]]
-
[[Category: Ligase-dna complex]]
+
[[Category: Shi K]]

Current revision

Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate

PDB ID 6dt1

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/6dt1"
Personal tools