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: 76.84 kDa 
• Atom Count: 5949 
• Modelled Residue Count: 641 
• Deposited Residue Count: 660 
• Unique protein chains: 3

3LU9

Crystal structure of human thrombin mutant S195A in complex with the extracellular fragment of human PAR1

• DOI: 10.2210/pdb3LU9/pdb

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


• Deposited: 2010-02-17 Released: 2010-03-16 
• Deposition Author(s): Gandhi, P.S., Chen, Z., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Crystal structure of thrombin bound to the uncleaved extracellular fragment of PAR1.

Gandhi, P.S., Chen, Z., Di Cera, E.

(2010) J Biol Chem 285: 15393-15398

• PubMed: 20236938 
• DOI: 10.1074/jbc.M110.115337
• Primary Citation of Related Structures:  
  3LU9


• PubMed Abstract: 
  

Abundant structural information exists on how thrombin recognizes ligands at the active site or at exosites separate from the active site region, but remarkably little is known about how thrombin recognizes substrates that bridge both the active site and exosite I. The case of the protease-activated receptor PAR1 is particularly relevant in view of the plethora of biological effects associated with its activation by thrombin. Here, we present the 1.8 A resolution structure of thrombin S195A in complex with a 30-residue long uncleaved extracellular fragment of PAR1 that documents for the first time a productive binding mode bridging the active site and exosite I. The structure reveals two unexpected features of the thrombin-PAR1 interaction. The acidic P3 residue of PAR1, Asp(39), does not hinder binding to the active site and actually makes favorable interactions with Gly(219) of thrombin. The tethered ligand domain shows a considerable degree of disorder even when bound to thrombin. The results fill a significant gap in our understanding of the molecular mechanisms of recognition by thrombin in ways that are relevant to other physiological substrates.

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Related Citations: 

• Molecular dissection of NA+ binding to thrombin
  Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z., Mathews, F.S., Di Cera, E.
  (2004) J Biol Chem 279: 31842

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A, D	46	Homo sapiens	Mutation(s): 0  Gene Names: F2, Human 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
Prothrombin	B, E	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 1	C, F	25	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth B], J [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	H [auth B], K [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.334	α = 76.39
b = 50.171	β = 83.93
c = 85.502	γ = 73.74

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-17 
• Released Date: 2010-03-16 
Deposition Author(s): Gandhi, P.S., Chen, Z., Di Cera, E.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary