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2A45

Crystal structure of the complex between thrombin and the central "E" region of fibrin

Replaces:  1QVH
Summary for 2A45
Entry DOI10.2210/pdb2a45/pdb
Related PRD IDPRD_000020
DescriptorThrombin light chain, Thrombin heavy chain, Fibrinogen alpha chain, ... (7 entities in total)
Functional Keywordsthrombin, fibrin, fragment e, thrombin-fibrin complex, coiled coils, disulfide rings, blood clotting, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
Biological sourceHomo sapiens (human)
More
Total number of polymer chains10
Total formula weight111917.71
Authors
Pechik, I.,Madrazo, J.,Gilliland, G.L.,Medved, L. (deposition date: 2005-06-27, release date: 2006-05-02, Last modification date: 2024-11-13)
Primary citationPechik, I.,Yakovlev, S.,Mosesson, M.W.,Gilliland, G.L.,Medved, L.
Structural basis for sequential cleavage of fibrinopeptides upon fibrin assembly.
Biochemistry, 45:3588-3597, 2006
Cited by
PubMed Abstract: Nonsubstrate interaction of thrombin with fibrinogen promotes sequential cleavage of fibrinopeptides A and B (fpA and fpB, respectively) from the latter, resulting in its conversion into fibrin. The recently established crystal structure of human thrombin in complex with the central part of human fibrin clarified the mechanism of this interaction. Here, we reveal new details of the structure and present the results of molecular modeling of the fpA- and fpB-containing portions of the Aalpha and Bbeta chains, not identified in the complex, in both fibrinogen and protofibrils. The analysis of the results reveals that in fibrinogen the fpA-containing portions are in a more favorable position to bind in the active site cleft of bound thrombin. Surface plasmon resonance experiments establish that the fpB-containing portions interact with the fibrin-derived dimeric D-D fragment, suggesting that in protofibrils they bind to the newly formed DD regions bringing fpB into the vicinity of bound thrombin. These findings provide a coherent rationale for the preferential removal of fpA from fibrinogen at the first stage of fibrin assembly and the accelerated cleavage of fpB from protofibrils and/or fibrils at the second stage.
PubMed: 16533041
DOI: 10.1021/bi0525369
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (3.65 Å)
Structure validation

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