Thrombin: Difference between revisions
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[[Image:Cation pi.png|450px|center|thumb| A cation-π interaction between Trp128 and Arg 129 in alpha thrombin (PDB: 2BDY). The guanidinium carbon is 3.6 angstroms from the top edge of the Trp. It is expected that the epsilon nitrogen forms the primary cation-π interaction. The electrostatic and Van der Waals interaction energies were calculated to be -3.29 kcal/mol and -3.08 kcal/mol respectively by the CaPTURE program (http://capture.caltech.edu/result.cgi).]] | [[Image:Cation pi.png|450px|center|thumb| A cation-π interaction between Trp128 and Arg 129 in alpha thrombin (PDB: 2BDY). The guanidinium carbon is 3.6 angstroms from the top edge of the Trp. It is expected that the epsilon nitrogen forms the primary cation-π interaction. The electrostatic and Van der Waals interaction energies were calculated to be -3.29 kcal/mol and -3.08 kcal/mol respectively by the CaPTURE program (http://capture.caltech.edu/result.cgi).]] | ||
{{Clear}} | {{Clear}} | ||
== 3D Structures of thrombin== | |||
[[Thrombin 3D Structures]] | |||
</StructureSection> | </StructureSection> | ||
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*'''Thrombin''' | *'''Thrombin''' | ||
**[[3r3g]], [[3gic]] - hThr HC + LC - human<br /> | |||
**[[3jz1]], [[3jz2]], [[2od3]] - hThr HC + LC (mutant) <br /> | |||
**[[3qgn]], [[4rkj]], [[5jdu]], [[6pxq]], [[6pxj], [[3ee0]], [[2a0q]], [[1sg8]], [[1sgi]], [[1jou]] - hThr HC (mutant) + LC<br /> | |||
**[[2hnt]]– hThr-γ HC + LC<br /> | |||
**[[3pmb]] - bThr HC + LC – bovine<br /> | **[[3pmb]] - bThr HC + LC – bovine<br /> | ||
**[[ | **[[2ocv]] - mThr HC + LC - mouse<br /> | ||
**[[3edx]], [[3hk3]], [[3hk6]] - mThr HC (mutant) + LC<br /> | |||
**[[3edx]], [[3hk3]], [[3hk6]] - mThr HC (mutant) + LC | |||
*Thrombin complexes with small molecule | *Thrombin complexes with small molecule | ||
**[[1bhx]], [[1abj]], [[1ppb]] - hThr HC + LC + inhibitor<br /> | **[[1bhx]], [[1abj]], [[1ppb]] - hThr HC + LC + inhibitor<br /> | ||
**[[4rn6]] - hThr HC (mutant) + inhibitor<br /> | **[[4rn6]] - hThr HC (mutant) + inhibitor<br /> | ||
**[[3dd2]] - hThr HC + LC + RNA<br /> | **[[3dd2]] - hThr HC + LC + RNA<br /> | ||
**[[1hao]], [[1hap]], [[1hut]] - hThr HC + LC + DNA<br /> | **[[1hao]], [[1hap]], [[1hut]] - hThr HC + LC + DNA<br /> | ||
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**[[1ook]] - hThr HC + LC + PPACK<BR /> | **[[1ook]] - hThr HC + LC + PPACK<BR /> | ||
**[[2hpp]], [[2hpq]] - hThr HC + LC + PThr residues 214-292 + PPACK<BR /> | **[[2hpp]], [[2hpq]] - hThr HC + LC + PThr residues 214-292 + PPACK<BR /> | ||
**[[3pma]] – bThr HC + LC residues 336-364 + sucrose octasulfate<br /> | |||
**[[1uvs]], [[1uvt]], [[1uvu]] - bThr HC + LC + inhibitor<br /> | |||
**[[1etr]], [[1ets]], [[1ett]] – bThr-ε HC + LC + inhibitor<br /> | |||
*Thrombin complexes with peptide | *Thrombin complexes with peptide | ||
**[[ | **[[5gim]] - hPThr HC + LC + peptide<br /> | ||
**[[3hkj]] - hThr HC (mutant) + LC + proteinase-activated receptor 1 peptide<br /> | **[[3hkj]] - hThr HC (mutant) + LC + proteinase-activated receptor 1 peptide<br /> | ||
**[[1fph]] - hThr HC + LC + fibrinogen peptide<br /> | **[[1fph]] - hThr HC + LC + fibrinogen peptide<br /> | ||
**[[3bv9]] - hThr HC (mutant) + LC + peptide inhibitor<br /> | **[[3bv9]] - hThr HC (mutant) + LC + peptide inhibitor<br /> | ||
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**[[4ch2]], [[4ch8]] - hThr HC + LC + platelet glycoprotein IB α chain peptide <br /> | **[[4ch2]], [[4ch8]] - hThr HC + LC + platelet glycoprotein IB α chain peptide <br /> | ||
**[[2ank]], [[3po1]] - hThr HC + LC + peptide + inhibitor<br /> | **[[2ank]], [[3po1]] - hThr HC + LC + peptide + inhibitor<br /> | ||
**[[ | **[[1dlk]] - bThr HC + LC + peptide inhibitor<br /> | ||
**[[1ycp]], [[1bbr]] – bThr-ε HC + LC + fibrinogen peptide<br /> | |||
**[[1ucy]] - bThr HC + LC + fibrinogen peptide<br /> | |||
**[[3hki]] - mThr HC (mutant) + LC + proteinase-activated receptor 1 peptide<br /> | |||
**[[2pux]] - mThr HC + LC + proteinase-activated receptor 3 peptide<br /> | |||
**[[2pv9]] - mThr HC (mutant) + LC + proteinase-activated receptor 4 peptide<br /> | |||
**[[1dm4]] - mThr HC (mutant) + LC + fibrinogen peptide<br /> | |||
*Thrombin complexes containing hirudin | *Thrombin complexes containing hirudin | ||
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**[[2a45]] - hThr HC + LC + fibrinogen α, β, γ chains<br /> | **[[2a45]] - hThr HC + LC + fibrinogen α, β, γ chains<br /> | ||
**[[1tb6]] - hThr HC + LC (mutant) + antithrombin<br /> | **[[1tb6]] - hThr HC + LC (mutant) + antithrombin<br /> | ||
**[[2b5t]] - hThr HC (mutant) + LC + antithrombin III (mutant)<br /> | **[[2b5t]] - hThr HC (mutant) + LC + antithrombin III (mutant)<br /> | ||
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**[[3pmh]] - hThr HC + LC + platelet glycoprotein IB α chain<br /> | **[[3pmh]] - hThr HC + LC + platelet glycoprotein IB α chain<br /> | ||
**[[3b23]] - hThr HC + LC + variegin<br /> | **[[3b23]] - hThr HC + LC + variegin<br /> | ||
**[[5e8e]] - hThr HC + LC + antibody<br /> | |||
**[[2a1d]], [[1nu7]] – bThr HC + LC + staphylocoagulase<br /> | |||
**[[1avg]] - bThr HC + LC + triabin<br /> | **[[1avg]] - bThr HC + LC + triabin<br /> | ||
**[[1bth]] - bThr HC (mutant) + LC (mutant) + BPTI<br /> | **[[1bth]] - bThr HC (mutant) + LC (mutant) + BPTI<br /> | ||
**[[1toc]] - bThr HC + LC + ornithodorin<br /> | **[[1toc]] - bThr HC + LC + ornithodorin<br /> | ||
**[[1tbq]], [[1tbr]] - bThr HC + LC + rhodniin<br /> | **[[1tbq]], [[1tbr]] - bThr HC + LC + rhodniin<br /> | ||
*'''Prothrombin''' | *'''Prothrombin''' | ||
