Primary Citation PubMed: 21715374
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Thrombin-aptamer recognition: a revealed ambiguity.
(2011) Nucleic Acids Res 39
PubMed: 21715374 | PubMedCentral: PMC3177225 | DOI: 10.1093/nar/gkr522
The coordinates of the structure have been deposited in the Protein Data Bank (Code 3QLP).
ACCESSION NUMBER 3QLP.
Publication Year: 2011
High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity.
(2012) Nucleic Acids Res 40
PubMed: 22669903 | PubMedCentral: PMC3439905 | DOI: 10.1093/nar/gks512
Despite the differences in the crystal packing and symmetry, the present crystal structures and those previously published for thrombin–TBA (1HAO) ( 33 , 34 ) and for thrombin–mTBA (3Q... P) ( 39 , 40 ) complexes present two invariant features: (a) the asymmetric unit contains one thrombin and one aptamer molecule and (b) apart from the 1HAO structure, the most extended interface between the two molecules is composed by the thrombin exosite I and the two TT loops of the aptamer ( Figure 3 ).
However, the binding mode on thrombin observed for TBA in the present structures differs by a 180° rotation about the helix axis when compared with thrombin–mTBA (PDB code 3QLP) and also with the old thrombin–TBA (PDB code 1HAO) structures ( Figure 5 ).
Structure determination and refinement The structure of thrombin–TBA–K was solved by the molecular replacement method using the program Phaser ( 42 ) and coordinates of both inhibited thrombin (derived from the structure of its complex with mTBA, PDB code 3QLP) and TBA (derived from the structure of the complex with thrombin, PDB code 1HAO) as search models.
Publication Year: 2012
Association of putative members to family of mosquito odorant binding proteins: scoring scheme using fuzzy functional templates and cys residue positions.
(2013) Bioinform Biol Insights 7
PubMed: 23908587 | PubMedCentral: PMC3728099 | DOI: 10.4137/BBI.S11096
29 For the serine protease family, 11 structural entries from the thrombin subfamily (1ai8, 1avg, 1hao, 1mkx, 1ucy, 2hpp, 3hk3, 3k65, 3nxp, 3pma, 3qlp), 15 structural entries from the trypsin family (... aoj, 1aks, 1an1, 1fxy, 1hj8, 1jrs, 1pq7, 2a31, 2eek, 2f91, 2ra3, 3beu, 3fp7, 3mi4, 3p95) and 4 structural entries from the plasminogen activator (1a5h, 1a5i, 1bqy, 1rtf) subfamily were used for the construction of the structural alignment.
Publication Year: 2013
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