4THN

THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE.

Summary for 4THN

• Entry DOI: 10.2210/pdb4thn/pdb
• Descriptor: ALPHA-THROMBIN, HIRUNORM IV, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: complex (serine protease-inhibitor), thrombin synthetic inhibitors, antithrombotics, hirudin-like binding mode, hirunorms, thrombin, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 37114.23

Authors

Lombardi, A.,De Simone, G.,Nastri, F.,Galdiero, S.,Della Morte, R.,Staiano, N.,Pedone, C.,Bolognesi, M.,Pavone, V. (deposition date: 1998-09-18, release date: 1999-06-15, Last modification date: 2023-08-09)

Primary citation

Lombardi, A.,De Simone, G.,Nastri, F.,Galdiero, S.,Della Morte, R.,Staiano, N.,Pedone, C.,Bolognesi, M.,Pavone, V.
The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode.
Protein Sci., 8:91-95, 1999

PubMed Abstract: The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 A resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which justifies the high inhibitory potency and the selectivity of hirunorm IV. This novel inhibitor, composed of 26 amino acids, interacts through the N-terminal end with the alpha-thrombin active site in a nonsubstrate mode, and binds specifically to the fibrinogen recognition exosite through the C-terminal end. The backbone of the N-terminal tripeptide Chg1"-Arg2"-2Na13" (Chg, cyclohexyl-glycine; 2Na1, beta-(2-naphthyl)-alanine) forms a parallel beta-strand to the thrombin main-chain segment Ser214-Gly216. The Chg1" side chain occupies the S2 site, Arg2" penetrates into the S1 specificity site, while the 2Na13" side chain occupies the aryl binding site. The Arg2" side chain enters the S1 specificity pocket from a position quite apart from the canonical P1 site. This notwithstanding, the Arg2" side chain establishes the typical ion pair with the carboxylate group of Asp189.

PubMed: 10210187

Experimental method

X-RAY DIFFRACTION (2.5 Å)