3BEI

Crystal structure of the slow form of thrombin in a self_inhibited conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural identification of the pathway of long-range communication in an allosteric enzyme.

Gandhi, P.S.Chen, Z.Mathews, F.S.Di Cera, E.

(2008) Proc.Natl.Acad.Sci.Usa 105: 1832-1837

  • DOI: 10.1073/pnas.0710894105
  • Primary Citation of Related Structures:  
  • Also Cited By: 3S7H, 3JZ2, 3JZ1

  • PubMed Abstract: 
  • Allostery is a common mechanism of regulation of enzyme activity and specificity, and its signatures are readily identified from functional studies. For many allosteric systems, structural evidence exists of long-range communication among protein dom ...

    Allostery is a common mechanism of regulation of enzyme activity and specificity, and its signatures are readily identified from functional studies. For many allosteric systems, structural evidence exists of long-range communication among protein domains, but rarely has this communication been traced to a detailed pathway. The thrombin mutant D102N is stabilized in a self-inhibited conformation where access to the active site is occluded by a collapse of the entire 215-219 beta-strand. Binding of a fragment of the protease activated receptor PAR1 to exosite I, 30-A away from the active site region, causes a large conformational change that corrects the position of the 215-219 beta-strand and restores access to the active site. The crystal structure of the thrombin-PAR1 complex, solved at 2.2-A resolution, reveals the details of this long-range allosteric communication in terms of a network of polar interactions.


    Related Citations: 
    • Crystal structure of the slow form of thrombin in a self-inhibited conformation
      Pineda, A.O.,Chen, Z.,Mathews, F.S.,Di Cera, E.
      (2006) J.Biol.Chem. 281: 32922


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
A
44Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
B
259Homo sapiensMutation(s): 1 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.193 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 57.980α = 90.00
b = 57.980β = 90.00
c = 120.201γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Database references