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.
1koc
From Proteopedia
| |||||||
| Ligands: | , , , , | ||||||
| Related: | 1KOD
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
RNA APTAMER COMPLEXED WITH ARGININE, NMR
Overview
In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.
About this Structure
1KOC is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy., Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M, Science. 1996 May 31;272(5266):1343-7. PMID:8650546
Page seeded by OCA on Sun Mar 30 21:51:21 2008
