3HKJ

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

• PDB DOI: https://doi.org/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 

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: 72.3 kDa 
• Atom Count: 4,864 
• Modelled Residue Count: 577 
• Deposited Residue Count: 622 
• Unique protein chains: 3

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
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, E	259	Homo sapiens	Mutation(s): 2  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 1	C, F	21	Homo sapiens	Mutation(s): 0  Gene Names: F2R, CF2R, PAR1, TR
UniProt & NIH Common Fund Data Resources
Find proteins for P25116 (Homo sapiens) Explore P25116  Go to UniProtKB:  P25116
PHAROS:  P25116 GTEx:  ENSG00000181104

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth B], H [auth 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

• 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
• Version 1.3: 2021-10-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description