PDBsum entry 1tmt

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Hydrolase/hydrolase inhibitor PDB id
Protein chains
27 a.a. *
258 a.a. *
11 a.a. *
Waters ×111
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Changes in interactions in complexes of hirudin derivatives alpha-thrombin due to different crystal forms
Structure: Alpha-thrombin (small subunit). Chain: l. Engineered: yes. Alpha-thrombin (large subunit). Chain: h. Engineered: yes. Cgp 50,856 inhibitor, cleaved n-terminal tripepti fragment, d-phe-pro-arg. Chain: i.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli.
Biol. unit: Not given
2.20Å     R-factor:   0.177    
Authors: J.P.Priestle,M.G.Gruetter
Key ref:
J.P.Priestle et al. (1993). Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms. Protein Sci, 2, 1630-1642. PubMed id: 8251938 DOI: 10.1002/pro.5560021009
26-May-94     Release date:   30-Sep-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
27 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
258 a.a.
Protein chain
Pfam   ArchSchema ?
P28504  (HIR2_HIRME) -  Hirudin-2
65 a.a.
11 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains L, 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: 10.1002/pro.5560021009 Protein Sci 2:1630-1642 (1993)
PubMed id: 8251938  
Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms.
J.P.Priestle, J.Rahuel, H.Rink, M.Tones, M.G.Grütter.
The three-dimensional structures of D-Phe-Pro-Arg-chloromethyl ketone-inhibited thrombin in complex with Tyr-63-sulfated hirudin (ternary complex) and of thrombin in complex with the bifunctional inhibitor D-Phe-Pro-Arg-Pro-(Gly)4-hirudin (CGP 50,856, binary complex) have been determined by X-ray crystallography in crystal forms different from those described by Skrzypczak-Jankun et al. (Skrzypczak-Jankun, E., Carperos, V.E., Ravichandran, K.G., & Tulinsky, A., 1991, J. Mol. Biol. 221, 1379-1393). In both complexes, the interactions of the C-terminal hirudin segments of the inhibitors binding to the fibrinogen-binding exosite of thrombin are clearly established, including residues 60-64, which are disordered in the earlier crystal form. The interactions of the sulfate group of Tyr-63 in the ternary complex structure explain why natural sulfated hirudin binds with a 10-fold lower K(i) than the desulfated recombinant material. In this new crystal form, the autolysis loop of thrombin (residues 146-150), which is disordered in the earlier crystal form, is ordered due to crystal contacts. Interactions between the C-terminal fragment of hirudin and thrombin are not influenced by crystal contacts in this new crystal form, in contrast to the earlier form. In the bifunctional inhibitor-thrombin complex, the peptide bond between Arg-Pro (P1-P1') seems to be cleaved.
  Selected figure(s)  
Figure 6.
Fig. 6. Residues h55-h58 of CGP 50,856 (solid bonds) with electron density in the exosite of thrombin (open bonds). The 2.2 2F0 - F,, UA (Read, 1986) electrondensitycon- toured at 1 rms above the meanslowly fades away beyond theamino side of residue h55, implying that the Pro- (Gly), linker of CGP 50,856 as well as residuh5extends out into the sol- vent in some disorderly fashionafter being cleaved. The side chain fh55- Aspcouldalsonotbeinterpreted from the electron density.
Figure 7.
Fig. 7. Conformation of the 149 loop in thrombin as found in three different crystal structures: PPACK-inhibited thrombin (open bonds; Bode et al., 1989), hirudin-inhibited thrombin (striped bonds; Grutter et al., 1990), andCGP 50,856-inhibited thrombin (solid bonds).
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1993, 2, 1630-1642) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19816721 Amorim, P.A.Netz, and J.A.Guimarães (2010).
Thrombin allosteric modulation revisited: a molecular dynamics study.
  J Mol Model, 16, 725-735.  
17685615 C.C.Liu, E.Brustad, W.Liu, and P.G.Schultz (2007).
Crystal structure of a biosynthetic sulfo-hirudin complexed to thrombin.
  J Am Chem Soc, 129, 10648-10649.
PDB code: 2pw8
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.  
11060016 J.L.Richardson, B.Kröger, W.Hoeffken, J.E.Sadler, P.Pereira, R.Huber, W.Bode, and P.Fuentes-Prior (2000).
Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor.
  EMBO J, 19, 5650-5660.
PDB code: 1e0f
10739913 R.Krishnan, J.E.Sadler, and A.Tulinsky (2000).
Structure of the Ser195Ala mutant of human alpha--thrombin complexed with fibrinopeptide A(7--16): evidence for residual catalytic activity.
  Acta Crystallogr D Biol Crystallogr, 56, 406-410.
PDB code: 1dm4
11053836 R.Recacha, M.J.Costanzo, B.E.Maryanoff, M.Carson, L.DeLucas, and D.Chattopadhyay (2000).
Structure of human alpha-thrombin complexed with RWJ-51438 at 1.7 A: unusual perturbation of the 60A-60I insertion loop.
  Acta Crystallogr D Biol Crystallogr, 56, 1395-1400.
PDB code: 1doj
10504391 T.Steinmetzer, M.Renatus, S.Künzel, A.Eichinger, W.Bode, P.Wikström, J.Hauptmann, and J.Stürzebecher (1999).
Design and evaluation of novel bivalent thrombin inhibitors based on amidinophenylalanines.
  Eur J Biochem, 265, 598-605.
PDB code: 1qur
  9521099 G.De Simone, A.Lombardi, S.Galdiero, F.Nastri, R.Della Morte, N.Staiano, C.Pedone, M.Bolognesi, and V.Pavone (1998).
Hirunorms are true hirudin mimetics. The crystal structure of human alpha-thrombin-hirunorm V complex.
  Protein Sci, 7, 243-253.
PDB code: 5gds
  9792427 S.Tada, and J.J.Blow (1998).
The replication licensing system.
  Biol Chem, 379, 941-949.  
9214615 A.van de Locht, W.Bode, R.Huber, B.F.Le Bonniec, S.R.Stone, C.T.Esmon, and M.T.Stubbs (1997).
The thrombin E192Q-BPTI complex reveals gross structural rearrangements: implications for the interaction with antithrombin and thrombomodulin.
  EMBO J, 16, 2977-2984.
PDB code: 1bth
  8868478 R.Krishnan, A.Tulinsky, G.P.Vlasuk, D.Pearson, P.Vallar, P.Bergum, T.K.Brunck, and W.C.Ripka (1996).
Synthesis, structure, and structure-activity relationships of divalent thrombin inhibitors containing an alpha-keto-amide transition-state mimetic.
  Protein Sci, 5, 422-433.
PDB code: 1dit
8569452 P.Ascenzi, G.Amiconi, W.Bode, M.Bolognesi, M.Coletta, and E.Menegatti (1995).
Proteinase inhibitors from the European medicinal leech Hirudo medicinalis: structural, functional and biomedical aspects.
  Mol Aspects Med, 16, 215-313.  
8001550 A.Vindigni, V.De Filippis, G.Zanotti, C.Visco, G.Orsini, and A.Fontana (1994).
Probing the structure of hirudin from Hirudinaria manillensis by limited proteolysis. Isolation, characterization and thrombin-inhibitory properties of N-terminal fragments.
  Eur J Biochem, 226, 323-333.  
  7756983 J.Vijayalakshmi, K.P.Padmanabhan, K.G.Mann, and A.Tulinsky (1994).
The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin.
  Protein Sci, 3, 2254-2271.
PDB codes: 1hag 1hah 1hai
7712286 M.T.Stubbs, and W.Bode (1994).
Coagulation factors and their inhibitors.
  Curr Opin Struct Biol, 4, 823-832.  
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.