Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 37.49 kDa 
• Atom Count: 2515 
• Residue Count: 305 
• Unique protein chains: 3

3B23

Crystal structure of thrombin-variegin complex: Insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors

• DOI: 10.2210/pdb3B23/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Amblyomma variegatum
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2011-07-20 Released: 2011-11-23 
• Deposition Author(s): Koh, C.Y., Kumar, S., Swaminathan, K., Kini, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Crystal structure of thrombin in complex with s-variegin: insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors

Koh, C.Y., Kumar, S., Kazimirova, M., Nuttall, P.A., Radhakrishnan, U.P., Kim, S., Jagadeeswaran, P., Imamura, T., Mizuguchi, J., Iwanaga, S., Swaminathan, K., Kini, R.M.

(2011) PLoS One 6: e26367-e26367

• PubMed: 22053189 
• DOI: 10.1371/journal.pone.0026367
• Primary Citation of Related Structures:  
  3B23


• PubMed Abstract: 
  

The inhibition of thrombin is one of the important treatments of pathological blood clot formation. Variegin, isolated from the tropical bont tick, is a novel molecule exhibiting a unique 'two-modes' inhibitory property on thrombin active site (competitive before cleavage, noncompetitive after cleavage). For the better understanding of its function, we have determined the crystal structure of the human α-thrombin:synthetic-variegin complex at 2.4 Å resolution. The structure reveals a new mechanism of thrombin inhibition by disrupting the charge relay system. Based on the structure, we have designed 17 variegin variants, differing in potency, kinetics and mechanism of inhibition. The most active variant is about 70 times more potent than the FDA-approved peptidic thrombin inhibitor, hirulog-1/bivalirudin. In vivo antithrombotic effects of the variegin variants correlate well with their in vitro affinities for thrombin. Our results encourage that variegin and the variants show strong potential for the development of tunable anticoagulants.

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Organizational Affiliation: 

Department of Biological Sciences, National University of Singapore, Singapore, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A	36	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	259	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Variegin	C	32	Amblyomma variegatum	Mutation(s): 0
Find proteins for P85800 (Amblyomma variegatum) Explore P85800  Go to UniProtKB:  P85800

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.658	α = 90
b = 50.826	β = 98.7
c = 61.535	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-20 
• Released Date: 2011-11-23 
Deposition Author(s): Koh, C.Y., Kumar, S., Swaminathan, K., Kini, R.M.

Revision History 

• Version 1.0: 2011-11-23
  Type: Initial release