Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
4i7y
Class
hydrolase-hydrolase inhibitor-DNA
Method
X-ray (2.4 Å)
Summary
Crystal structure of human alpha thrombin in complex with a 27-mer aptamer bound to exosite ii
Reference
Russo Krauss, I., Pica, A., Merlino, A., Mazzarella, L., Sica, F.: (2013) "Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer." Acta Crystallogr.,Sect.D, 69, 2403-2411.
Abstract
Potent second-generation thrombin aptamers adopt a duplex-quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and control their recruitment in thrombin binding.
G4 notes
1 G-tetrad

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 1 G-tetrad [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=-s-s groove=wnwn planarity=0.842 type=other  nts=4 GGGG D.DG8,D.DG20,D.DG17,D.DG11

List of 0 G4-helices [summary · schematics · tetrads · stems · costacks · homepage]

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

List of 0 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 3 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#-1 nts=4 GTAG D.DG8,D.DT9,D.DA10,D.DG11
 2 type=lateral   helix=#-1 nts=7 GGGCAGG D.DG11,D.DG12,D.DG13,D.DC14,D.DA15,D.DG16,D.DG17
 3 type=lateral   helix=#-1 nts=4 GTTG D.DG17,D.DT18,D.DT19,D.DG20