Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.30 kDa 
• Atom Count: 4864 
• Residue Count: 577 
• Unique protein chains: 3

3HKJ

Crystal structure of human thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1

• DOI: 10.2210/pdb3HKJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2009-05-23 Released: 2009-07-07 
• Deposition Author(s): Gandhi, P.S., Page, M.J., Chen, Z., Bush-Pelc, L., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A.

Gandhi, P.S., Page, M.J., Chen, Z., Bush-Pelc, L., Di Cera, E.

(2009) J Biol Chem 284: 24098-24105

• PubMed: 19586901 
• DOI: 10.1074/jbc.M109.025403
• Primary Citation of Related Structures:  
  3HK3, 3HKI, 3HKJ, 3HK6


• PubMed Abstract: 
  

The thrombin mutant W215A/E217A (WE) is a potent anticoagulant both in vitro and in vivo. Previous x-ray structural studies have shown that WE assumes a partially collapsed conformation that is similar to the inactive E* form, which explains its drastically reduced activity toward substrate. Whether this collapsed conformation is genuine, rather than the result of crystal packing or the mutation introduced in the critical 215-217 beta-strand, and whether binding of thrombomodulin to exosite I can allosterically shift the E* form to the active E form to restore activity toward protein C are issues of considerable mechanistic importance to improve the design of an anticoagulant thrombin mutant for therapeutic applications. Here we present four crystal structures of WE in the human and murine forms that confirm the collapsed conformation reported previously under different experimental conditions and crystal packing. We also present structures of human and murine WE bound to exosite I with a fragment of the platelet receptor PAR1, which is unable to shift WE to the E form. These structural findings, along with kinetic and calorimetry data, indicate that WE is strongly stabilized in the E* form and explain why binding of ligands to exosite I has only a modest effect on the E*-E equilibrium for this mutant. The E* --> E transition requires the combined binding of thrombomodulin and protein C and restores activity of the mutant WE in the anticoagulant pathway.

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Related Citations: 

• The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket.
  Pineda, A.O., Chen, Z.W., Caccia, S., Cantwell, A.M., Savvides, S.N., Waksman, G., Mathews, F.S., Di Cera, E.
  (2004) J Biol Chem 279: 39824

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A, D	31	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B, E	259	Homo sapiens	Mutation(s): 2  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase-activated receptor 1	C, F	21	Homo sapiens	Mutation(s): 0  Gene Names: F2R, CF2R, PAR1, TR
Find proteins for P25116 (Homo sapiens) Explore P25116  Go to UniProtKB:  P25116
NIH Common Fund Data Resources
PHAROS:  P25116 GTEx:  ENSG00000181104

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B, E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.14	α = 98.78
b = 61.783	β = 110.28
c = 67.834	γ = 92.95

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-23 
• Released Date: 2009-07-07 
Deposition Author(s): Gandhi, P.S., Page, M.J., Chen, Z., Bush-Pelc, L., Di Cera, E.

Revision History 

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary