1HUT image
Deposition Date 1993-05-27
Release Date 1994-06-22
Last Version Date 2024-10-16
Entry Detail
PDB ID:
1HUT
Title:
THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ALPHA-Thrombin heavy chain
Gene (Uniprot):F2
Chain IDs:C (auth: H)
Chain Length:259
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:ALPHA-Thrombin light chain
Gene (Uniprot):F2
Chain IDs:B (auth: L)
Chain Length:36
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Peptide-like Molecules
PRD_000021
Primary Citation
The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer.
J.Biol.Chem. 268 17651 17654 (1993)
PMID: 8102368

Abstact

The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crystallography and refined at 2.9-A resolution to an R value of 0.159. As in solution, in the complex the single-stranded DNA folds into a structure with two G-quartets. The DNA is sandwiched between two different positively charged regions of two symmetry-related thrombin molecules in the crystal structure making ionic and hydrophobic interactions. One region is the fibrinogen recognition exosite and the other, the putative heparin binding site. The lack of inhibition of fibrinogen clotting and platelet activation by the DNA 15-mer with the Arg75-->Glu mutant of thrombin is consistent with the several salt bridges of the DNA in the fibrinogen exosite. The association of DNA with the heparin site of a neighboring molecule appears to simply compensate residual charge. Differences in the 15-mer loop conformations between the complex and NMR solution structures can be attributed to conformational changes upon thrombin binding. Although G-quadruplexes are favored in the presence of monovalent cations, there is no evidence of the latter in the thrombin complex.

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Primary Citation of related structures