1HLT

THE STRUCTURE OF A NONADECAPEPTIDE OF THE FIFTH EGF DOMAIN OF THROMBOMODULIN COMPLEXED WITH THROMBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of a nonadecapeptide of the fifth EGF domain of thrombomodulin complexed with thrombin.

Mathews, I.I.Padmanabhan, K.P.Tulinksy, A.Sadler, J.E.

(1994) Biochemistry 33: 13547-13552

  • DOI: 10.1021/bi00250a006
  • Primary Citation of Related Structures:  
    1HLT

  • PubMed Abstract: 
  • The crystallographic structure has been determined of a complex between a nonadecapeptide from the fifth epidermal growth factor (EGF5) domain of human thrombomodulin and human D-PheProArg-alpha-thrombin. The peptide corresponds to amino acid residues Glu408-Glu426 of thrombomodulin and contains the third disulfide loop of EGF5 and its linker to EGF6 ...

    The crystallographic structure has been determined of a complex between a nonadecapeptide from the fifth epidermal growth factor (EGF5) domain of human thrombomodulin and human D-PheProArg-alpha-thrombin. The peptide corresponds to amino acid residues Glu408-Glu426 of thrombomodulin and contains the third disulfide loop of EGF5 and its linker to EGF6. The structure was refined at 3.0-A resolution to an R-value of 0.146. There are two thrombin molecules in the asymmetric unit, and the structure in the crystal is a 2:1 thrombin complex. The folding of the peptide corresponds closely to the third disulfide loop of EGF2 of factor Xa (rms delta = 1.0 A). The peptide is squeezed between cofacial electropositive fibrinogen recognition exo sites of the two thrombin molecules. Since the peptide has a total of seven aspartic and glutamic acid residues, the principal binding interaction with thrombin is electrostatic. A major hydrophobic association, which is highly directional in such a pronounced electrostatic environment, involves a TyrIleLeu triplet of the peptide and Phe34, Leu65, Tyr76, and Ile82 (chymotrypsinogen numbering) of one thrombin molecule. The tyrosine of the peptide is sandwiched between the thrombin aromatic rings and is most likely the prime source of the specificity of the thrombomodulin-thrombin interaction.


    Related Citations: 
    • Alanine-Scanning Mutagenesis of the Epidermal Growth Factor-Like Domains of Human Thrombomodulin Identifies Critical Residues for its Cofactor Activity
      Nagashima, M., Lundh, E., Leonard, J.C., Parkinson, J.F.
      (1993) J Biol Chem 268: 2888
    • Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin
      Skrzypczak-Jankun, E., Carperos, V.E., Ravichandran, K.G., Tulinsky, A., Westbrook, M., Maraganore, J.M.
      (1991) J Mol Biol 221: 1379

    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing 48824-1322.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-THROMBIN (SMALL SUBUNIT) JL27Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-THROMBIN (LARGE SUBUNIT) HK259Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombomodulin R19N/AMutation(s): 0 
Find proteins for P07204 (Homo sapiens)
Explore P07204 
Go to UniProtKB:  P07204
NIH Common Fund Data Resources
PHAROS:  P07204
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G6
Query on 0G6

Download Ideal Coordinates CCD File 
H, K
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
C21 H34 Cl N6 O3
DVFLYEYCMMLBTQ-VSZNYVQBSA-O
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020
H, KD-Phe-Pro-Arg-CH2ClPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.9α = 90
b = 50.9β = 90
c = 325.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-12-20
    Type: Initial release
  • Version 1.1: 2008-03-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 1.4: 2019-07-17
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description