1EB1

Complex structure of human thrombin with N-methyl-arginine inhibitor

Summary for 1EB1

• Entry DOI: 10.2210/pdb1eb1/pdb
• Related: 1A2C 1A3B 1A3E 1A46 1A4W 1A5G 1A61 1ABI 1ABJ 1AD8 1AE8 1AFE 1AHT 1AI8 1AIX 1AWF 1AWH 1AY6 1B5G 1B7X 1BA8 1BB0 1BCU 1BHX 1BMM 1BMN 1BTH 1C1U 1C1V 1C1W 1C4U 1C4V 1C4Y 1C5L 1C5N 1C5O 1CA8 1D3D 1D3P 1D3Q 1D3T 1D4P 1D6W 1D9I 1DE7 1DIT 1DM4 1DOJ 1DWB 1DWC 1DWD 1DWE 1DX5 1E0F 1EOJ 1EOL 1FPC 1FPH 1G37 1H8D 1H8I 1HAG 1HAH 1HAI 1HAO 1HAP 1HBT 1HDT 1HGT 1HLT 1HUT 1HXE 1HXF 1IHS 1IHT 1LHC 1LHD 1LHE 1LHF 1LHG 1NRN 1NRO 1NRP 1NRQ 1NRR 1NRS 1PPB 1QBV 1QHR 1QJ1 1QJ6 1QJ7 1QUR 1TBZ 1THP 1THR 1THS 1TMB 1TMT 1TMU 1TOM 1UMA 1UVS 1VR1 2HGT 2HNT 2HPP 2HPQ 2THF 3HAT 3HTC 4HTC 4THN 5GDS 7KME 8KME
• Related PRD ID: PRD_000616
• Descriptor: PEPTIDE INHIBITOR, THROMBIN HEAVY CHAIN, THROMBIN LIGHT CHAIN, ... (5 entities in total)
• Functional Keywords: serine proteinase, blood coagulation, calcium-binding, glycoprotein, kringle, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: HOMO SAPIENS (HUMAN); More
• Total number of polymer chains: 4
• Total formula weight: 34430.50

Authors

Friedrich, R.,Steinmetzer, T.,Bode, W. (deposition date: 2001-07-18, release date: 2002-01-28, Last modification date: 2023-12-13)

Primary citation

Friedrich, R.,Steinmetzer, T.,Huber, R.,Sturzebecher, J.,Bode, W.
The Methyl Group of N(Alpha)(Me)Arg-Containing Peptides Disturbs the Active-Site Geometry of Thrombin, Impairing Efficient Cleavage
J.Mol.Biol., 316:869-, 2002

PubMed Abstract: Bivalent peptidic thrombin inhibitors consisting of an N-terminal d-cyclohexylalanine-Pro-N(alpha)(Me)Arg active-site fragment, a flexible polyglycine linker, and a C-terminal hirugen-like segment directed towards the fibrinogen recognition exosite inhibit thrombin with K(i) values in the picomolar range, remaining stable in buffered solution at pH 7.8 for at least 15 hours. In order to investigate the structural basis of this increased stability, the most potent of these inhibitors, I-11 (K(i)=37pM), containing an N(alpha)(Me)Arg-Thr bond, was crystallized in complex with human alpha-thrombin. X-ray data were collected to 1.8A resolution and the crystal structure of this complex was determined. The Fourier map displays clear electron density for the N-terminal fragment and for the exosite binding segment. It indicates, however, that in agreement with Edman sequencing, the peptide had been cleaved in the crystal, presumably due to the long incubation time of 14 days needed for crystallization and data collection. The N(alpha)(Me) group is directed toward the carbonyl oxygen atom of Ser214, pushing the Ser195 O(gamma) atom out of its normal site. This structure suggests that upon thrombin binding, the scissile peptide bond of the intact peptide and the Ser195 O(gamma) are separated from each other, impairing the nucleophilic attack of the Ser195 O(gamma) toward the N(alpha)(Me)Arg carbonyl group. In the time-scale of two weeks, however, cleavage geometries favoured by the crystal allow catalysis at a slow rate.

PubMed: 11884127
DOI: 10.1006/JMBI.2001.5394

Experimental method

X-RAY DIFFRACTION (1.8 Å)