3BV9

Structure of Thrombin Bound to the Inhibitor FM19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Thrombostatin FM compounds: direct thrombin inhibitors - mechanism of action in vitro and in vivo.

Nieman, M.T.Burke, F.Warnock, M.Zhou, Y.Sweigart, J.Chen, A.Ricketts, D.Lucchesi, B.R.Chen, Z.Di Cera, E.Hilfinger, J.Kim, J.S.Mosberg, H.I.Schmaier, A.H.

(2008) J Thromb Haemost 6: 837-845

  • DOI: 10.1111/j.1538-7836.2008.02937.x
  • Primary Citation of Related Structures:  
    3BV9

  • PubMed Abstract: 
  • Novel pentapeptides called Thrombostatin FM compounds consisting mostly of D-isomers and unusual amino acids were prepared based upon the stable angiotensin converting enzyme breakdown product of bradykinin - RPPGF.


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

    Organizational Affiliation

    Division of Hematology and Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106-7284, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chainA31N/AMutation(s): 0 
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
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 chainB259Homo sapiensMutation(s): 1 
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
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FM19 inhibitorC6N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download CCD File 
B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4PH
Query on 4PH
CL-PEPTIDE LINKINGC10 H13 N O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000276
Query on PRD_000276
CThrombostatin FM inhibitor [rOicPaF(p-Me)]Peptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.907α = 90
b = 80.907β = 90
c = 183.718γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other