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.


4ypm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:24, 3 May 2023) (edit) (undo)
 
Line 1: Line 1:
==Crystal structure of a LonA protease domain in complex with bortezomib==
==Crystal structure of a LonA protease domain in complex with bortezomib==
-
<StructureSection load='4ypm' size='340' side='right' caption='[[4ypm]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+
<StructureSection load='4ypm' size='340' side='right'caption='[[4ypm]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4ypm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_baa-399 Atcc baa-399]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YPM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4ypm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Meiothermus_taiwanensis Meiothermus taiwanensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YPM FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BO2:N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE'>BO2</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BO2:N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE'>BO2</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ypl|4ypl]], [[4ypn|4ypn]]</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=4ypm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypm OCA], [https://pdbe.org/4ypm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ypm RCSB], [https://www.ebi.ac.uk/pdbsum/4ypm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypm ProSAT]</span></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lonA1, lon ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=172827 ATCC BAA-399])</td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_La Endopeptidase La], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.53 3.4.21.53] </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=4ypm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypm OCA], [http://pdbe.org/4ypm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ypm RCSB], [http://www.ebi.ac.uk/pdbsum/4ypm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypm ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/A0A059VAZ3_9DEIN A0A059VAZ3_9DEIN]] ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner.[HAMAP-Rule:MF_01973]
+
[https://www.uniprot.org/uniprot/A0A059VAZ3_9DEIN A0A059VAZ3_9DEIN] ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner.[HAMAP-Rule:MF_01973]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 25: Line 22:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc baa-399]]
+
[[Category: Large Structures]]
-
[[Category: Endopeptidase La]]
+
[[Category: Meiothermus taiwanensis]]
-
[[Category: Chang, C I]]
+
[[Category: Chang C-I]]
-
[[Category: Lin, C C]]
+
[[Category: Lin C-C]]
-
[[Category: Aaa+ domain]]
+
-
[[Category: Bortezomib]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Lon protease]]
+
-
[[Category: Magnesium]]
+
-
[[Category: Protease domain]]
+

Current revision

Crystal structure of a LonA protease domain in complex with bortezomib

PDB ID 4ypm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools