ISDA

Entry Detail

PDB ID:

4I7Y

Keywords:

HYDROLASE/HYDROLASE INHIBITOR/DNA

Title:

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

Biological Source:

Source Organism:

SYNTHETIC DNA, Homo sapiens

PDB Version:

Deposition Date:

2012-12-01

Release Date:

2013-10-16

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.40 Å

R-Value Free:

0.24

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 1 21 1

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Description:DNA (27-MER)
Chain IDs:C (auth: D)
Chain Length:27
Number of Molecules:1
Biological Source:SYNTHETIC DNA

Protein Blast

Polymer Type:polypeptide(L)
Description:Prothrombin
Chain IDs:A (auth: H)
Chain Length:259
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P00734 Pfam ID:PF00089, PF09396 EC:3.4.21.5

Protein Blast

Polymer Type:polypeptide(L)
Description:Prothrombin
Chain IDs:B (auth: L)
Chain Length:36
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P00734 Pfam ID:PF00089, PF09396 EC:3.4.21.5

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
ASN	A	ASN	GLYCOSYLATION SITE

Ligand Molecules

0G6

NAG

Peptide-like Molecules

PRD_000020

Primary Citation

Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer.

Russo Krauss, I, Pica, A, Merlino, A, Mazzarella, L, Sica, F, Russo Krauss, I, Merlino, A, Giancola, C, Randazzo, A, Mazzarella, L, Sica, F, Russo Krauss, I, Merlino, A, Randazzo, A, Novellino, E, Mazzarella, L, Sica, F.Show

Acta Crystallogr.,Sect.D 69 2403 2411 (2013)

PMID: 24311581 DOI: 10.1107/S0907444913022269

Abstact

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.

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Primary Citation of related structures