5f3z

From Proteopedia

(Difference between revisions)

Revision as of 07:58, 29 April 2020

Dengue serotype 3 RNA-dependent RNA polymerase bound to PC-79-SH52

Structural highlights

5f3z is a 1 chain structure with sequence from Dengue virus 3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	5f3t, 5f41
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q6DLV0_9FLAV] Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).[SAAS:SAAS000336_004_099774]

Publication Abstract from PubMed

We performed a fragment screen on the dengue virus serotype 3 RNA-dependent RNA polymerase using X-ray crystallography. A screen of 1,400 fragments in pools of 8 identified a single hit that bound in a novel pocket in the protein. This pocket is located in the polymerase palm sub-domain and conserved across the four serotypes of dengue virus. The compound binds to the polymerase in solution as evidenced by surface-plasmon resonance and isothermal titration calorimetry analyses. Related compounds where a phenyl is replaced by a thiophene, show higher-affinity binding, indicating the potential for rational design. Importantly, inhibition of enzyme activity correlated with the binding affinity, showing that the pocket is functionally important for polymerase activity. This fragment is an excellent starting point for optimization through rational structure-based design.

A Conserved Pocket in the Dengue Virus Polymerase Identified Through Fragment-Based Screening.,Noble CG, Lim SP, Arora R, Yokokawa F, Nilar S, Seh CC, Wright SK, Benson TE, Smith PW, Shi PY J Biol Chem. 2016 Feb 12. pii: jbc.M115.710731. PMID:26872970^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Noble CG, Lim SP, Arora R, Yokokawa F, Nilar S, Seh CC, Wright SK, Benson TE, Smith PW, Shi PY. A Conserved Pocket in the Dengue Virus Polymerase Identified Through Fragment-Based Screening. J Biol Chem. 2016 Feb 12. pii: jbc.M115.710731. PMID:26872970 doi:http://dx.doi.org/10.1074/jbc.M115.710731

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5f3z"

@@ Line 1: / Line 1: @@
 ==Dengue serotype 3 RNA-dependent RNA polymerase bound to PC-79-SH52==
-<StructureSection load='5f3z' size='340' side='right' caption='[[5f3z]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5f3z' size='340' side='right'caption='[[5f3z]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5f3z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F3Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5f3z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus_3 Dengue virus 3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F3Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5F3Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5V5:2-(4-METHOXY-3-THIOPHEN-2-YL-PHENYL)ETHANOIC+ACID'>5V5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5V5:2-(4-METHOXY-3-THIOPHEN-2-YL-PHENYL)ETHANOIC+ACID'>5V5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5f3t|5f3t]], [[5f41|5f41]]</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=5f3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f3z OCA], [http://pdbe.org/5f3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f3z RCSB], [http://www.ebi.ac.uk/pdbsum/5f3z PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5f3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f3z OCA], [http://pdbe.org/5f3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f3z RCSB], [http://www.ebi.ac.uk/pdbsum/5f3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f3z ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Dengue virus 3]]
+[[Category: Large Structures]]
 [[Category: Noble, C G]]
 [[Category: Dengue]]
 [[Category: Rdrp inhibitor]]
 [[Category: Transferase]]

5f3z

From Proteopedia

Revision as of 07:58, 29 April 2020

Dengue serotype 3 RNA-dependent RNA polymerase bound to PC-79-SH52

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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