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.
1k8n
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1k8n |SIZE=350|CAPTION= <scene name='initialview01'>1k8n</scene> | |PDB= 1k8n |SIZE=350|CAPTION= <scene name='initialview01'>1k8n</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=C2S:CYTIDINE-5'-DITHIOPHOSPHORATE'>C2S</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1k8j|1K8J]], [[1k8l|1K8L]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k8n OCA], [http://www.ebi.ac.uk/pdbsum/1k8n PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1k8n RCSB]</span> | ||
}} | }} | ||
| Line 38: | Line 41: | ||
[[Category: xby6]] | [[Category: xby6]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:44:53 2008'' |
Revision as of 18:44, 30 March 2008
| |||||||
| Ligands: | , , , , | ||||||
| Related: | 1K8J, 1K8L
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24
Overview
A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experiments. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our hypothesis that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-kappaB homo- and heterodimers suggests that the dithioate backbone substitution can increase the aptamer's relative affinity to basic groups in proteins such as NF-kappaB by helping to "strip" the cations from the aptamer backbone.
About this Structure
1K8N is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB., Volk DE, Yang X, Fennewald SM, King DJ, Bassett SE, Venkitachalam S, Herzog N, Luxon BA, Gorenstein DG, Bioorg Chem. 2002 Dec;30(6):396-419. PMID:12642125
Page seeded by OCA on Sun Mar 30 21:44:53 2008
Categories: Protein complex | Bassett, S E. | Fennewald, S M. | Gorenstein, D G. | Herzog, N. | King, D J. | Luxon, B A. | Venkitachalam, S. | Volk, D E. | Yang, X. | Ck1 | Ck14 | Nf-kb | Phosphorodithioate | Thiophosphate | Xby2 | Xby6
