3QDZ

Crystal structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR4.

• PDB DOI: https://doi.org/10.2210/pdb3QDZ/pdb

• Classification: HYDROLASE/HYDROLASE RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Mesocricetus auratus
• Mutation(s): Yes 


• Deposited: 2011-01-19 Released: 2011-06-29 
• Deposition Author(s): Gandhi, P., Chen, Z., Appelbaum, E., Zapata, F., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.364 
• R-Value Work: 0.304 

Starting Model: experimental

Literature

Structural basis of thrombin-protease-receptor interactions

Gandhi, P.S., Chen, Z., Appelbaum, E., Zapata, F., Di Cera, E.

(2011) IUBMB Life 63: 375-382

Biological Assembly 1  

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

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

Biological Assembly 2  

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: 68.76 kDa 
• Atom Count: 4,677 
• Modelled Residue Count: 579 
• Deposited Residue Count: 598 
• Unique protein chains: 3

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B, D	259	Homo sapiens	Mutation(s): 1  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase-activated receptor 4	E, F	9	Homo sapiens	Mutation(s): 0  Gene Names: F2RL3, PAR4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI0 (Homo sapiens) Explore Q96RI0  Go to UniProtKB:  Q96RI0
PHAROS:  Q96RI0 GTEx:  ENSG00000127533

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.364 
• R-Value Work: 0.304 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.414	α = 90
b = 102.876	β = 90
c = 146.39	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Gandhi, P., Chen, Z., Appelbaum, E., Zapata, F., Di Cera, E.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary