4I7Y

Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II

Summary for 4I7Y

• Entry DOI: 10.2210/pdb4i7y/pdb
• Related: 3QLP 4DIH 4DII
• Related PRD ID: PRD_000020
• Descriptor: Prothrombin, DNA (27-MER), D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, ... (7 entities in total)
• Functional Keywords: protein-dna complex, serine protease, blood coagulation, aptamer, hydrolase-hydrolase inhibitor-dna complex, serine protease fold, dna aptamer, blood, g-quadruplex, duplex-quadruplex junction, hydrolase/hydrolase inhibitor/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 43060.37

Authors

Pica, A.,Russo Krauss, I.,Merlino, A.,Mazzarella, L.,Sica, F. (deposition date: 2012-12-01, release date: 2013-10-16, Last modification date: 2024-10-09)

Primary citation

Russo Krauss, I.,Pica, A.,Merlino, A.,Mazzarella, L.,Sica, F.
Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer.
Acta Crystallogr.,Sect.D, 69:2403-2411, 2013

PubMed 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.

PubMed: 24311581
DOI: 10.1107/S0907444913022269

Experimental method

X-RAY DIFFRACTION (2.4 Å)