6TKJ

Tsetse thrombin inhibitor in complex with human alpha-thrombin - tetragonal form at 7keV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Sulfotyrosine-Mediated Recognition of Human Thrombin by a Tsetse Fly Anticoagulant Mimics Physiological Substrates.

Calisto, B.M.Ripoll-Rozada, J.Dowman, L.J.Franck, C.Agten, S.M.Parker, B.L.Veloso, R.C.Vale, N.Gomes, P.de Sanctis, D.Payne, R.J.Pereira, P.J.B.

(2021) Cell Chem Biol 28: 26

  • DOI: 10.1016/j.chembiol.2020.10.002
  • Primary Citation of Related Structures:  
    6TKG, 6TKH, 6TKI, 6TKJ, 6TKL

  • PubMed Abstract: 
  • Despite possessing only 32 residues, the tsetse thrombin inhibitor (TTI) is among the most potent anticoagulants described, with sub-picomolar inhibitory activity against thrombin. Unexpectedly, TTI isolated from the fly is 2000-fold more active and 180 Da heavier than synthetic and recombinant variants ...

    Despite possessing only 32 residues, the tsetse thrombin inhibitor (TTI) is among the most potent anticoagulants described, with sub-picomolar inhibitory activity against thrombin. Unexpectedly, TTI isolated from the fly is 2000-fold more active and 180 Da heavier than synthetic and recombinant variants. We predicted the presence of a tyrosine O-sulfate post-translational modification of TTI, prompting us to investigate the effect of the modification on anticoagulant activity. A combination of chemical synthesis and functional assays was used to reveal that sulfation significantly improved the inhibitory activity of TTI against thrombin. Using X-ray crystallography, we show that the N-terminal sulfated segment of TTI binds the basic exosite II of thrombin, establishing interactions similar to those of physiologic substrates, while the C-terminal segment abolishes the catalytic activity of thrombin. This non-canonical mode of inhibition, coupled with its potency and small size, makes TTI an attractive scaffold for the design of novel antithrombotics.


    Organizational Affiliation

    IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal. Electronic address: ppereira@ibmc.up.pt.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chainA [auth L]36Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chainB [auth H]259Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tsetse thrombin inhibitorC [auth I]53Glossina morsitans morsitansMutation(s): 0 
Gene Names: TTI
UniProt
Find proteins for O97373 (Glossina morsitans morsitans)
Explore O97373 
Go to UniProtKB:  O97373
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
D [auth H]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
C [auth I]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 
  • Space Group: P 41 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/740 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.977α = 90
b = 114.977β = 90
c = 62.512γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)AustraliaAPP1120941
Fundacao para a Ciencia e a TecnologiaPortugal57/2016/CP1355/CT0011

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references