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.
1vy5
From Proteopedia
(Difference between revisions)
| Line 4: | Line 4: | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1vy5]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcq 4qcq], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcr 4qcr], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcs 4qcs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qct 4qct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VY5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[1vy5]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcq 4qcq], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcr 4qcr], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcs 4qcs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qct 4qct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VY5 FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=31M:3-DEOXY-3-[(L-METHIONYL-L-PHENYLALANYL)AMINO]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>31M</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.55Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=31M:3-DEOXY-3-[(L-METHIONYL-L-PHENYLALANYL)AMINO]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>31M</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1vy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vy5 OCA], [https://pdbe.org/1vy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vy5 RCSB], [https://www.ebi.ac.uk/pdbsum/1vy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vy5 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=1vy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vy5 OCA], [https://pdbe.org/1vy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vy5 RCSB], [https://www.ebi.ac.uk/pdbsum/1vy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vy5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| Line 20: | Line 21: | ||
==See Also== | ==See Also== | ||
| + | *[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]] | ||
| + | *[[Ribosome 3D structures|Ribosome 3D structures]] | ||
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | ||
== References == | == References == | ||
Current revision
Crystal structure of the Thermus thermophilus 70S ribosome in the post-catalysis state of peptide bond formation containing dipeptydil-tRNA in the A site and deacylated tRNA in the P site.
| |||||||||||
