PDBsum entry 1xmn

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protein ligands metals Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
Protein chains
31 a.a. *
256 a.a. *
32 a.a. *
29 a.a. *
31 a.a. *
0G6 ×4
GOL ×8
_NA ×4
Waters ×750
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure of thrombin bound to heparin
Structure: Thrombin light chain. Chain: a, c, e, g. Synonym: coagulation factor ii. Thrombin heavy chain. Chain: b, d, f, h. Synonym: coagulation factor ii. Ec:
Source: Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 9606
Biol. unit: Trimer (from PQS)
1.85Å     R-factor:   0.209     R-free:   0.234
Authors: W.J.Carter,E.Cama,J.A.Huntington
Key ref:
W.J.Carter et al. (2005). Crystal structure of thrombin bound to heparin. J Biol Chem, 280, 2745-2749. PubMed id: 15548541 DOI: 10.1074/jbc.M411606200
04-Oct-04     Release date:   23-Nov-04    
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Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
31 a.a.
Protein chains
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
256 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
32 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
29 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
31 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.  - Thrombin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     blood coagulation   2 terms 
  Biochemical function     catalytic activity     3 terms  


DOI no: 10.1074/jbc.M411606200 J Biol Chem 280:2745-2749 (2005)
PubMed id: 15548541  
Crystal structure of thrombin bound to heparin.
W.J.Carter, E.Cama, J.A.Huntington.
Thrombin is the final protease in the blood coagulation cascade and serves both pro- and anticoagulant functions through the cleavage of several targets. The ability of thrombin to specifically recognize a wide range of substrates derives from interactions that occur outside of the active site of thrombin. Thrombin possesses two anion binding exosites, which mediate many of its interactions with cofactors and substrates, and although many structures of thrombin have been solved, few such interactions have been described in molecular detail. Glycosaminoglycan binding to exosite II of thrombin plays a major role in switching off the procoagulant functions of thrombin by mediating its irreversible inhibition by circulating serpins and by its binding to the endothelial cell surface receptor thrombomodulin. Here we report the 1.85-A structure of human alpha-thrombin bound to a heparin fragment of eight monosaccharide units in length. The asymmetric unit is composed of two thrombin dimers, each sharing a single heparin octasaccharide chain. The observed interactions are fully consistent with previous mutagenesis studies and illustrate on a molecular level the cofactor interaction that is critical for the restriction of clotting to the site of blood vessel injury.
  Selected figure(s)  
Figure 1.
FIG. 1. Ribbon and surface electrostatic representations of thrombin bound to heparin. A, the asymmetric unit consists of four thrombin monomers organized into two nearly equivalent dimers. Because -thrombin is a two-chain molecule, each monomer is denoted by two letters according to the chain ID of the light and heavy chains, with blue corresponding to monomer AB, red to monomer CD, orange to monomer EF, and cyan to monomer GH. Each monomer is inhibited by PPACK, shown in green space-filling. Two heparin chains were independently built (ball-and-stick) between the dimer partners in opposite orientations. B, the most intimate contact with heparin (ball-and-stick) was found for monomer AB (surface representation colored according to electrostatic potential, with blue for positive and red for negative). Thrombin is oriented so that exosite II is facing, and some of the contacting residues are labeled (Lys236 was not fully modeled in electron density and was rebuilt here for the purpose of illustrating its contribution to the surface electrostatics). The confidence in the positioning of the heparin fragment is demonstrated by the 2F[o] - F[c] electron density map (green) shown surrounding the modeled hexasaccharide fragment.
Figure 2.
FIG. 2. Schematic of observed contacts between the two heparin chains and the four thrombin monomers of the asymmetric unit. Six heparin monosaccharide units were built into the electron density between monomers AB and GH (A), and five were built between monomers CD and EF (B). In both dimers, monomers in equivalent positions (AB and CD) make them most intimate contacts with heparin, with minimal contacts observed between heparin and the other pair of equivalent monomers (EF and GH, see Fig. 1A). All contacts are between heparin and atoms on the side chains of indicated thrombin residues, with the exception of a main chain hydrogen bond for Trp237 (dotted line). The line style denotes the type of interaction: with a solid line indicating a salt bridge, a dashed line indicating a hydrogen bond, a dotted-dashed line indicating a water-mediated hydrogen bond, and a jagged dotted line indicating potential ionic interactions for incompletely built side chains. The packing of the monomers against one another placed Lys236 into close approximation with the same residue of the dimer partner, resulting in its disorder in the crystal structure.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 2745-2749) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21524910 J.G.Zhou, and Y.M.Chen (2011).
Research on PEGylation of porcine prothrombin for improving biostability and reducing animal immunogenicity.
  Bioorg Med Chem Lett, 21, 3268-3272.  
20080729 D.J.Johnson, J.Langdown, and J.A.Huntington (2010).
Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-A structure of the ternary complex.
  Proc Natl Acad Sci U S A, 107, 645-650.
PDB code: 3kcg
20002544 N.J.Mutch, T.Myles, L.L.Leung, and J.H.Morrissey (2010).
Polyphosphate binds with high affinity to exosite II of thrombin.
  J Thromb Haemost, 8, 548-555.  
19589779 N.S.Petrera, A.R.Stafford, B.A.Leslie, C.A.Kretz, J.C.Fredenburgh, and J.I.Weitz (2009).
Long range communication between exosites 1 and 2 modulates thrombin function.
  J Biol Chem, 284, 25620-25629.  
19528533 Z.Wei, Y.Yan, R.W.Carrell, and A.Zhou (2009).
Crystal structure of protein Z-dependent inhibitor complex shows how protein Z functions as a cofactor in the membrane inhibition of factor X.
  Blood, 114, 3662-3667.
PDB code: 3f1s
18329094 E.Di Cera (2008).
  Mol Aspects Med, 29, 203-254.  
18364727 K.P.Doyle, T.Yang, N.S.Lessov, T.M.Ciesielski, S.L.Stevens, R.P.Simon, J.S.King, and M.P.Stenzel-Poore (2008).
Nasal administration of osteopontin peptide mimetics confers neuroprotection in stroke.
  J Cereb Blood Flow Metab, 28, 1235-1248.  
18722183 L.Sanglas, Z.Valnickova, J.L.Arolas, I.Pallarés, T.Guevara, M.Solà, T.Kristensen, J.J.Enghild, F.X.Aviles, and F.X.Gomis-Rüth (2008).
Structure of activated thrombin-activatable fibrinolysis inhibitor, a molecular link between coagulation and fibrinolysis.
  Mol Cell, 31, 598-606.
PDB code: 3d4u
18854941 M.E.Papaconstantinou, P.S.Gandhi, Z.Chen, A.Bah, and E.Di Cera (2008).
Na+ binding to meizothrombin desF1.
  Cell Mol Life Sci, 65, 3688-3697.
PDB code: 3e6p
18971322 S.B.Long, M.B.Long, R.R.White, and B.A.Sullenger (2008).
Crystal structure of an RNA aptamer bound to thrombin.
  RNA, 14, 2504-2512.
PDB code: 3dd2
18779330 S.Lancellotti, S.Rutella, V.De Filippis, N.Pozzi, B.Rocca, and R.De Cristofaro (2008).
Fibrinogen-elongated gamma chain inhibits thrombin-induced platelet response, hindering the interaction with different receptors.
  J Biol Chem, 283, 30193-30204.  
18974053 W.Li, and J.A.Huntington (2008).
The Heparin Binding Site of Protein C Inhibitor Is Protease-dependent.
  J Biol Chem, 283, 36039-36045.
PDB code: 3dy0
18362344 W.Li, T.E.Adams, J.Nangalia, C.T.Esmon, and J.A.Huntington (2008).
Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex.
  Proc Natl Acad Sci U S A, 105, 4661-4666.
PDB code: 3b9f
17804413 B.L.Henry, B.H.Monien, P.E.Bock, and U.R.Desai (2007).
A novel allosteric pathway of thrombin inhibition: Exosite II mediated potent inhibition of thrombin by chemo-enzymatic, sulfated dehydropolymers of 4-hydroxycinnamic acids.
  J Biol Chem, 282, 31891-31899.  
17347701 E.Di Cera, M.J.Page, A.Bah, L.A.Bush-Pelc, and L.C.Garvey (2007).
Thrombin allostery.
  Phys Chem Chem Phys, 9, 1291-1306.  
17635727 E.Di Cera (2007).
Thrombin as procoagulant and anticoagulant.
  J Thromb Haemost, 5, 196-202.  
17878169 K.Segers, B.Dahlbäck, P.E.Bock, G.Tans, J.Rosing, and G.A.Nicolaes (2007).
The role of thrombin exosites I and II in the activation of human coagulation factor V.
  J Biol Chem, 282, 33915-33924.  
17635714 P.E.Bock, P.Panizzi, and I.M.Verhamme (2007).
Exosites in the substrate specificity of blood coagulation reactions.
  J Thromb Haemost, 5, 81-94.  
17414213 S.T.Lord (2007).
Fibrinogen and fibrin: scaffold proteins in hemostasis.
  Curr Opin Hematol, 14, 236-241.  
18077410 Y.Wu, C.Eigenbrot, W.C.Liang, S.Stawicki, S.Shia, B.Fan, R.Ganesan, M.T.Lipari, and D.Kirchhofer (2007).
Structural insight into distinct mechanisms of protease inhibition by antibodies.
  Proc Natl Acad Sci U S A, 104, 19784-19789.
PDB codes: 2r0k 2r0l
16759098 A.Raghuraman, P.D.Mosier, and U.R.Desai (2006).
Finding a needle in a haystack: development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s).
  J Med Chem, 49, 3553-3562.  
16619025 D.J.Johnson, W.Li, T.E.Adams, and J.A.Huntington (2006).
Antithrombin-S195A factor Xa-heparin structure reveals the allosteric mechanism of antithrombin activation.
  EMBO J, 25, 2029-2037.
PDB code: 2gd4
16102053 J.A.Huntington (2005).
Molecular recognition mechanisms of thrombin.
  J Thromb Haemost, 3, 1861-1872.  
15892855 W.Bode (2005).
The structure of thrombin, a chameleon-like proteinase.
  J Thromb Haemost, 3, 2379-2388.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.