PDBsum entry 1jou

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Blood clotting PDB id
Protein chains
45 a.a. *
259 a.a. *
47 a.a. *
NDG ×2
GOL ×4
ACY ×5
_NA ×3
Waters ×372
* Residue conservation analysis
PDB id:
Name: Blood clotting
Title: Crystal structure of native s195a thrombin with an unoccupie site
Structure: Thrombin, light chain. Chain: a, c, e. Fragment: factor xa cleavage product light chain. Synonym: coagulation factor ii. Engineered: yes. Other_details: contains extra 13 amino acids at the n-termi thrombin, heavy chain. Chain: b, d, f. Fragment: factor xa cleavage product heavy chain.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: bhk culture. Expression_system_organ: kidney. Expression_system_organ: kidney
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.222     R-free:   0.245
Authors: J.A.Huntington,C.T.Esmon
Key ref:
J.A.Huntington and C.T.Esmon (2003). The molecular basis of thrombin allostery revealed by a 1.8 A structure of the "slow" form. Structure, 11, 469-479. PubMed id: 12679024 DOI: 10.1016/S0969-2126(03)00049-2
31-Jul-01     Release date:   10-Aug-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
45 a.a.
Protein chains
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
259 a.a.*
Protein chains
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
47 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: 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: 10.1016/S0969-2126(03)00049-2 Structure 11:469-479 (2003)
PubMed id: 12679024  
The molecular basis of thrombin allostery revealed by a 1.8 A structure of the "slow" form.
J.A.Huntington, C.T.Esmon.
Thrombin participates in its own positive and negative feedback loops, and its allosteric state helps determine the hemostatic balance. Here we present the 1.8 A crystallographic structure of S195A thrombin in two conformational states: active site occupied and active site free. The active site-occupied form shows how thrombin can accommodate substrates, such as protein C. The active site-free form is in a previously unobserved closed conformation of thrombin, which satisfies all the conditions of the so-called "slow" form. A mechanism of allostery is revealed, which relies on the concerted movement of the disulphide bond between Cys168 and 182 and aromatic residues Phe227, Trp215, and Trp60d. These residues constitute an allosteric switch, which is flipped directly through sodium binding, resulting in the fast form with an open active site.
  Selected figure(s)  
Figure 3.
Figure 3. Stereo Representation of Surface Contours of the Thrombin Active Site PocketThrombin is shown in the classical "Bode" orientation, with the active site facing and the substrate binding from left to right for N- to C-terminal. The 60-insertion loop is located above the substrate. The surface contours are colored according to hydrophobicity, with green indicating the presence of an exposed hydrophobic side chain. The substrate binding site is indicated in (A) by the inclusion of the reactive center loop P4-P4' of HCII in complex with S195A thrombin (1jmo), and the peptide is removed for comparison in (B). Allosterically activated thrombin (C) is represented by the active site-free, hirugen-bound form (1hah) and is nearly identical to that of the substrate-bound form in (B). In contrast, the active site cleft of molecule EF (D) is significantly different, primarily because of the position of side chains Trp60d and Trp215 (Figure 2). Comparing substrate-bound thrombin in (A) to the substrate-free form in (D) reveals a complete occlusion of the P2 and aryl binding pocket in the active site-free monomer, EF. Thus, the active site of EF is in a closed conformation.
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 469-479) copyright 2003.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21360607 H.C.Castro, P.A.Abreu, R.B.Geraldo, R.C.Martins, R.Dos Santos, N.I.Loureiro, L.M.Cabral, and C.R.Rodrigues (2011).
Looking at the proteases from a simple perspective.
  J Mol Recognit, 24, 165-181.  
19816721 Amorim, P.A.Netz, and J.A.Guimarães (2010).
Thrombin allosteric modulation revisited: a molecular dynamics study.
  J Mol Model, 16, 725-735.  
19703402 N.Halabi, O.Rivoire, S.Leibler, and R.Ranganathan (2009).
Protein sectors: evolutionary units of three-dimensional structure.
  Cell, 138, 774-786.  
19656282 T.E.Adams, W.Li, and J.A.Huntington (2009).
Molecular basis of thrombomodulin activation of slow thrombin.
  J Thromb Haemost, 7, 1688-1695.
PDB code: 3gis
18329094 E.Di Cera (2008).
  Mol Aspects Med, 29, 203-254.  
18979627 J.A.Huntington (2008).
How Na+ activates thrombin--a review of the functional and structural data.
  Biol Chem, 389, 1025-1035.  
18393757 M.V.Kolodzeiskaya, L.I.Sokolovskaya, and G.L.Volkov (2008).
Role of A-chain in functioning of the active site of human alpha-thrombin.
  Biochemistry (Mosc), 73, 237-244.  
17635715 J.T.Crawley, S.Zanardelli, C.K.Chion, and D.A.Lane (2007).
The central role of thrombin in hemostasis.
  J Thromb Haemost, 5, 95.  
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.  
17635698 Y.M.Fortenberry, H.C.Whinna, S.T.Cooper, T.Myles, L.L.Leung, and F.C.Church (2007).
Essential thrombin residues for inhibition by protein C inhibitor with the cofactors heparin and thrombomodulin.
  J Thromb Haemost, 5, 1486-1492.  
16973611 D.J.Johnson, J.Langdown, W.Li, S.A.Luis, T.P.Baglin, and J.A.Huntington (2006).
Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation.
  J Biol Chem, 281, 35478-35486.
PDB codes: 1t1f 2b5t 2beh
16367756 R.De Cristofaro, A.Carotti, S.Akhavan, R.Palla, F.Peyvandi, C.Altomare, and P.M.Mannucci (2006).
The natural mutation by deletion of Lys9 in the thrombin A-chain affects the pKa value of catalytic residues, the overall enzyme's stability and conformational transitions linked to Na+ binding.
  FEBS J, 273, 159-169.  
16934999 S.M.Truhlar, C.H.Croy, J.W.Torpey, J.R.Koeppe, and E.A.Komives (2006).
Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry.
  J Am Soc Mass Spectrom, 17, 1490-1497.  
16487178 S.Rouy, D.Vidaud, J.L.Alessandri, M.D.Dautzenberg, L.Venisse, M.C.Guillin, and A.Bezeaud (2006).
Prothrombin Saint-Denis: a natural variant with a point mutation resulting in Asp to Glu substitution at position 552 in prothrombin.
  Br J Haematol, 132, 770-773.  
15892855 W.Bode (2005).
The structure of thrombin, a chameleon-like proteinase.
  J Thromb Haemost, 3, 2379-2388.  
15548541 W.J.Carter, E.Cama, and J.A.Huntington (2005).
Crystal structure of thrombin bound to heparin.
  J Biol Chem, 280, 2745-2749.
PDB code: 1xmn
15152000 A.O.Pineda, C.J.Carrell, L.A.Bush, S.Prasad, S.Caccia, Z.W.Chen, F.S.Mathews, and E.Di Cera (2004).
Molecular dissection of Na+ binding to thrombin.
  J Biol Chem, 279, 31842-31853.
PDB codes: 1sfq 1sg8 1sgi 1shh
14722067 R.De Cristofaro, S.Akhavan, C.Altomare, A.Carotti, F.Peyvandi, and P.M.Mannucci (2004).
A natural prothrombin mutant reveals an unexpected influence of A-chain structure on the activity of human alpha-thrombin.
  J Biol Chem, 279, 13035-13043.  
15075325 W.J.Carter, T.Myles, C.S.Gibbs, L.L.Leung, and J.A.Huntington (2004).
Crystal structure of anticoagulant thrombin variant E217K provides insights into thrombin allostery.
  J Biol Chem, 279, 26387-26394.
PDB code: 1rd3
12871289 J.A.Huntington (2003).
Mechanisms of glycosaminoglycan activation of the serpins in hemostasis.
  J Thromb Haemost, 1, 1535-1549.  
14607082 J.A.Huntington, and T.P.Baglin (2003).
Targeting thrombin--rational drug design from natural mechanisms.
  Trends Pharmacol Sci, 24, 589-595.  
12968031 T.H.Yun, F.A.Baglia, T.Myles, D.Navaneetham, J.A.López, P.N.Walsh, and L.L.Leung (2003).
Thrombin activation of factor XI on activated platelets requires the interaction of factor XI and platelet glycoprotein Ib alpha with thrombin anion-binding exosites I and II, respectively.
  J Biol Chem, 278, 48112-48119.  
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.