Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66458.16 
• Atom Count: 4494 
• Residue Count: 574 
• Unique protein chains: 1

1MH0

Crystal structure of the anticoagulant slow form of thrombin

• DOI: 10.2210/pdb1MH0/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): 1 


• Deposited: 2002-08-18 Released: 2002-11-08 
• Deposition Author(s): Pineda, A.O., Savvides, S., Waksman, G., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.275 
• R-Value Work: 0.219 

Literature

Crystal structure of the anticoagulant slow form of thrombin

Pineda, A.O., Savvides, S., Waksman, G., Di Cera, E.

(2002) J.Biol.Chem. 277: 40177-40180

• PubMed: 12205081 
• DOI: 10.1074/jbc.C200465200


• PubMed Abstract: 
  

Using the thrombin mutant R77aA devoid of the site of autoproteolytic degradation at exosite I, we have solved for the first time the structure of thrombin free of any inhibitors and effector molecules and stabilized in the Na(+)-free slow form. The slow form shows subtle differences compared with the currently available structures of the Na(+)-bound fast form that carry inhibitors at the active site or exosite I. The most notable differences are the displacement of Asp-189 in the S1 specificity pocket, a downward shift of the 190-193 strand, a rearrangement of the side chain of Glu-192, and a significant shift in the position of the catalytic Ser-195 that is no longer within H-bonding distance from His-57. The structure of the slow form explains the reduced specificity toward synthetic and natural substrates and suggests a molecular basis for its anticoagulant properties.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Prothrombin	A, B	287	Homo sapiens	Mutation(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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.275 
• R-Value Work: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 60.530	α = 90.00
b = 72.890	β = 90.00
c = 161.490	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	phasing
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-08-18 
• Released Date: 2002-11-08 
• Deposition Author(s): Pineda, A.O., Savvides, S., Waksman, G., Di Cera, E.

Revision History 

• Version 1.0: 2002-11-08
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance