3zcv: Difference between revisions

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 ==Rabbit muscle glycogen phosphorylase b in complex with N-(indol-2- carbonyl)-N-beta-D-glucopyranosyl urea determined at 1.8 A resolution==
-<StructureSection load='3zcv' size='340' side='right' caption='[[3zcv]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
+<StructureSection load='3zcv' size='340' side='right'caption='[[3zcv]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3zcv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZCV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZCV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3zcv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZCV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZCV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N85:N-[(1H-INDOL-2-YLCARBONYL)CARBAMOYL]-BETA-D-GLUCOPYRANOSYLAMINE'>N85</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.83&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3zcp|3zcp]], [[3zcq|3zcq]], [[3zcr|3zcr]], [[3zcs|3zcs]], [[3zct|3zct]], [[3zcu|3zcu]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N85:N-[(1H-INDOL-2-YLCARBONYL)CARBAMOYL]-BETA-D-GLUCOPYRANOSYLAMINE'>N85</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </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=3zcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zcv OCA], [https://pdbe.org/3zcv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zcv RCSB], [https://www.ebi.ac.uk/pdbsum/3zcv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zcv 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=3zcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zcv OCA], [http://pdbe.org/3zcv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zcv RCSB], [http://www.ebi.ac.uk/pdbsum/3zcv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zcv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PYGM_RABIT PYGM_RABIT]] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
+[https://www.uniprot.org/uniprot/PYGM_RABIT PYGM_RABIT] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Two substituted ureas of beta-D-glucose, N-acetyl-N'-beta-D-glucopyranosyl urea (Acurea) and N-benzoyl-N'-beta-D-glucopyranosyl urea (Bzurea), have been identified as inhibitors of glycogen phosphorylase, a potential target for therapeutic intervention in type 2 diabetes. To elucidate the structural basis of inhibition, we determined the structure of muscle glycogen phosphorylase b (GPb) complexed with the two compounds at 2.0 A and 1.8 A resolution, respectively. The structure of the GPb-Acurea complex reveals that the inhibitor can be accommodated in the catalytic site of T-state GPb with very little change in the tertiary structure. The glucopyranose moiety makes the standard hydrogen bonds and van der Waals contacts as observed in the GPb-glucose complex, while the acetyl urea moiety is in a favourable electrostatic environment and makes additional polar contacts with the protein. The structure of the GPb-Bzurea complex shows that Bzurea binds tightly at the catalytic site and induces substantial conformational changes in the vicinity of the catalytic site. In particular, the loop of the polypeptide chain containing residues 282-287 shifts 1.3-3.7 A (Calpha atoms) to accommodate Bzurea. Bzurea can also occupy the new allosteric site, some 33 A from the catalytic site, which is currently the target for the design of antidiabetic drugs.
-Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies.,Oikonomakos NG, Kosmopoulou M, Zographos SE, Leonidas DD, Chrysina ED, Somsak L, Nagy V, Praly JP, Docsa T, Toth B, Gergely P Eur J Biochem. 2002 Mar;269(6):1684-96. PMID:11895439<ref>PMID:11895439</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3zcv" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Glycogen Phosphorylase|Glycogen Phosphorylase]]
+*[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Phosphorylase]]
+[[Category: Alexacou KM]]
-[[Category: Alexacou, K M]]
+[[Category: Chrysina ED]]
-[[Category: Chrysina, E D]]
+[[Category: Docsa T]]
-[[Category: Docsa, T]]
+[[Category: Felfoldi N]]
-[[Category: Felfoldi, N]]
+[[Category: Gergely P]]
-[[Category: Gergely, P]]
+[[Category: Hayes JM]]
-[[Category: Hayes, J M]]
+[[Category: Kardakaris R]]
-[[Category: Kardakaris, R]]
+[[Category: Konstantakaki M]]
-[[Category: Konstantakaki, M]]
+[[Category: Konya B]]
-[[Category: Konya, B]]
+[[Category: Leonidas DD]]
-[[Category: Leonidas, D D]]
+[[Category: Nagy V]]
-[[Category: Nagy, V]]
+[[Category: Oikonomakos NG]]
-[[Category: Oikonomakos, N G]]
+[[Category: Praly JP]]
-[[Category: Praly, J P]]
+[[Category: Somsak L]]
-[[Category: Somsak, L]]
+[[Category: Telepo K]]
-[[Category: Telepo, K]]
+[[Category: Zographos SE]]
-[[Category: Zographos, S E]]
-[[Category: Hypoglycaemic agent]]
-[[Category: Inhibitor]]
-[[Category: N-acyl-n-beta-d-glucopyranosyl urea]]
-[[Category: Structure- based ligand design]]
-[[Category: Transferase]]