X-Ray Structures

  • 2THF, 1B7X, 1THP
    Unexpected crucial role of residue 225 in serine proteases. Guinto et al (1999) Proc Natl Acad Sci USA 96, 1852-1857.
  • 1MHO
    Crystal structure of the anticoagulant slow form of thrombin. Pineda et al (2002) J Biol Chem 277, 40177-40180.
  • 1SGI, 1SHH, 1SG8, 1SFQ
    Molecular dissection of Na+ binding to thrombin. Pineda et al (2004) J Biol Chem 279, 31842-31853.
  • 1TQ0, 1TQ7
    The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket. Pineda et al (2004) J Biol Chem 279, 39824-39828.
  • 1TWX
    Crystal structure of the thrombin mutant D221A/D222K: The Asp222:Arg187 ion-pair stabilizes the fast form. Pineda et al (2004) Biophys Chem 112, 253-256.
  • 1T31, 1T32
    A novel, potent dual inhibitor of the leukocyte proteases cathepsin G and chymase: molecular mechanisms and anti-inflammatory activity in vivo. de Garavilla et al (2005) J Biol Chem 280, 18001-18007.
  • 1Z8I, 1Z8J
    Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases. Bobofchak et al (2005) J Biol Chem 280, 25644-25650.
  • 2A0Q
    Thrombin functions through its RGD sequence in a non-canonical conformation. Papaconstantinou et al (2005) J Biol Chem 280, 29393-29396.
  • 2FMJ
    Conversion of trypsin into a Na+-activated enzyme. Page et al (2006) Biochemistry 45, 2987-2993.
  • 2GP9
    Crystal structure of thrombin in a self-inhibited conformation. Pineda et al (2006) J Biol Chem 281, 32922-32928.
  • 2HWL
    Crystal structure of thrombin in complex with fibrinogen gamma’ peptide. Pineda et al (2007) Biophys Chem 125, 556-559.
  • 2HVX
    Discovery of potent, selective, orally active, nonpeptide inhibitors of human mast cell chymase. Greco et al (2007) J Med Chem 50, 1527-1530.
  • 2OCV, 2OD3
    Structural basis of Na+ activation mimicry in murine thrombin. Marino et al (2007) J Biol Chem 282, 16355-16361.
  • 2PUX, 2PV9
    Crystal structures of murine thrombin in complex with the extracellular fragments of protease-activated receptors PAR3 and PAR4. Bah et al (2007) Proc Natl Acad Sci USA 104, 11603-11608.
  • 2PGB, 2PGQ
    Important role of the Cys-191:Cys-220 disulfide bond in thrombin function and allostery. Bush-Pelc et al (2007) J Biol Chem 282, 27165-27170.
  • 3BEI, 3BEF
    Structural identification of the pathway of long-range communication in an allosteric enzyme. Gandhi et al (2008) Proc Natl Acad Sci USA 105, 1832-1837.
  • 3BEU
    Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na+-activated trypsin. Page et al (2008) J Mol Biol 378, 666-672.
  • 3BV9
    Thrombostatin FM compounds: direct thrombin inhibitors – mechanism of action in vitro and in vivo. Nieman et al (2008) J Thromb Haemost 6, 837-845.
  • 3E6P
    Na+ binding to meizothrombin desF1. Papaconstantinou et al (2008) Cell Mol Life Sci 65, 3688-3697.
  • 3GIC
    Stabilization of the E* form turns thrombin into an anticoagulant. Bah et al (2009) J Biol Chem 284, 20034-20040.
  • 3HK3, 3HK6, 3HKI, 3HKJ, 3EDX, 3EE0
    Mechanism of the anticoagulant activity of the thrombin mutant W215A/E217A. Gandhi et al (2009) J Biol Chem 284, 24098-24105.
  • 3JZ1, 3JZ2
    The mutant N143P reveals how Na+ activates thrombin. Niu et al (2009) J Biol Chem 284, 36175-36185.
  • 3LU9
    Crystal structure of thrombin bound to the uncleaved extracellular fragment of PAR1. Gandhi et al (2010) J Biol Chem 285, 15393-15398.
  • 3I77, 3I78
    Combinatorial enzyme design probes allostery and cooperativity in the trypsin fold. Page MJ and Di Cera E (2010) J Mol Biol 399, 306-319.
  • 3MVT
    The role of Zn2+ on the structure and stability of murine adenosine deaminase. Niu et al (2010) J Phys Chem B 114, 16156-16165.
  • 3NXP
    Crystal structure of prethrombin-1. Chen et al (2010) Proc Natl Acad Sci U S A 107, 19278-19283.
  • 3QDZ
    Structural basis of thrombin-PAR interactions. Gandhi et al (2011) IUBMB Life 63, 375-382.
  • 3QGN, 3S7H, 3S7K
    Crystallographic and kinetic evidence of allostery in a trypsin-like protease. Niu et al (2011) Biochemistry 50, 6301-6307.
  • 3R3G
    Rigidification of the autolysis loop enhances Na+ binding to thrombin. Pozzi et al (2011) Biophys Chem 159, 6-13.
  • 3SQE, 3SQH
    Crystal structures of prethrombin-2 reveal alternative conformations under identical solution conditions and the mechanism of zymogen activation. Pozzi et al (2011) Biochemistry 50, 10195-10202.
  • 4DT7
    Exposure of R169 controls protein C activation and autoactivation. Pozzi et al (2012) Blood 120, 664-670.
  • 4H6T, 4RN6, 4H6S, 4HFP
    Autoactivation of thrombin precursors. Pozzi N et al. (2013) J Biol Chem, 288, 11601-11610.
  • 4HZH
    Crystal structure of prothrombin reveals conformational flexibility and mechanism of action. Pozzi N et al. (2013) J Biol Chem, 288, 22734-22744.
  • 4MLF
    Essential role of conformational selection in ligand binding. Vogt AD et al. (2014) Biophys Chem. 186, 13-21.
  • 4NZQ, 4O03
    The linker connecting the two kringles plays a key role in prothrombin activation. Pozzi N et al. (2014) Proc Natl Acad Sci USA. 111, 7630-7635.
  • 4RKJ, 4RKO
    Why ser and not thr brokers catalysis in the trypsin fold. Pelc L et al. (2015) Biochemistry. 54, 1457-1464.
  • 5EDK
    How the linker connecting the two Kringles influences activation and conformational plasticity of prothrombin. Pozzi N et al. (2016) J Biol Chem. 291, 6071-6082.
  • 5EDM
    Structural architecture of prothrombin in solution revealed by single molecule spectroscopy. Pozzi N et al. (2016) J Biol Chem. 291, 18107-18116.
  • 5JDU
    Loop electrostatics asymmetry modulates the preexisting conformational equilibrium in thrombin. Pozzi N et al. (2016) Biochemistry. 55, 3984-3994.
  • 5TO3
    Rational design of protein C activators. Barranco-Medina S et al. (2017) Sci Rep. 7, 44596-44597.
  • 5IPZ
    Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV. Mickeviciute A et al. (2017) Eur Biophys. 47, 271-290.
  • 6BJR, 6C2W
    Structure of prothrombin in the closed form reveals new details on the mechanism of activation. Chinnaraj et al. (2018) Sci Rep 8, 2945.
  • 6P9U
    Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Pelc LA et al. (2019) Sci Rep 9, 12304.
  • 6PXJ, 6PXQ
    Role of the I16-D194 ionic interaction in the trypsin fold. Stojanovski BM et al. (2019) Sci Rep 9, 18035.
  • 7KVE, 7KXY
    Cryo-EM structures of human coagulation factors V and Va. Ruben EA et al. (2021) Blood. 137, 3137-3144.
  • 7SR9
    The active site region plays a critical role in Na+ binding to thrombin. Pelc LA et al. (2021) J Biol Chem. 298, 101458.
  • 7TPQ, 7TPP
    Cryo-EM structure of the prothrombin-prothrombinase complex. Ruben EA et al. (2022) Blood. 139, 3463-3473.