1UCY

THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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Literature

Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues.

Martin, P.D.Malkowski, M.G.DiMaio, J.Konishi, Y.Ni, F.Edwards, B.F.

(1996) Biochemistry 35: 13030-13039

  • DOI: 10.1021/bi960656y
  • Primary Citation of Related Structures:  
    1UCY

  • PubMed Abstract: 
  • The crystal structure of the noncovalent complex of bovine thrombin and a fibrinogen-A alpha tridecapeptide substrate analog, G17 psi, in which the scissile bond amide nitrogen of Gly-17f has been replaced by a methylene carbon, has been determined at 2.3 A resolution with an R factor of 17 ...

    The crystal structure of the noncovalent complex of bovine thrombin and a fibrinogen-A alpha tridecapeptide substrate analog, G17 psi, in which the scissile bond amide nitrogen of Gly-17f has been replaced by a methylene carbon, has been determined at 2.3 A resolution with an R factor of 17.1%. The geometry of the active site indicates that the crystal structure is a close model of the true Michaelis complex. The three independently determined thrombin/G17 psi complexes in the crystal asymmetric unit reveal novel interactions for the P2' and P3' residues-Pro-18f and Arg-19f, respectively-on the carboxyl-terminal side of the scissile bond and confirm previously observed interactions of the P1 (Arg-16f) through P10 (Asp-7f) positions on the amino-terminal side. The thrombin S2' binding site for Pro-18f, as observed in all three complexes, differs from that predicted by modeling studies and is notable for including two carbonyl oxygens of the thrombin main chain. Arg-19f occupies two binding sites on thrombin, S3'A and S3'B, which have dramatically different placements for the arginyl side chain and carboxyl terminus.


    Organizational Affiliation

    Department of Biochemistry, Wayne State University, Detroit, Michigan 48201, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBINE [auth J], A [auth L], H [auth M]49Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBINB [auth H]150Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBINC [auth E]109Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRINOPEPTIDE A-ALPHAD [auth F], G, J [auth I]13N/AMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBINF [auth K], I [auth N]259Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.47α = 90
b = 88.78β = 106.21
c = 98.55γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
XENGENdata reduction
X-PLORrefinement
XENGENdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance