1HUT

THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer.

Padmanabhan, K., Padmanabhan, K.P., Ferrara, J.D., Sadler, J.E., Tulinsky, A.

(1993) J Biol Chem 268: 17651-17654

  • DOI: 10.2210/pdb1hut/pdb
  • Primary Citation of Related Structures:  
    1HUT

  • PubMed Abstract: 

    • The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crystallography and refined at 2.9-A resolution to an R value of 0.159. As in solution, in the complex the single-stranded DNA folds into a structure with two G-quartets ...

    The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crystallography and refined at 2.9-A resolution to an R value of 0.159. As in solution, in the complex the single-stranded DNA folds into a structure with two G-quartets. The DNA is sandwiched between two different positively charged regions of two symmetry-related thrombin molecules in the crystal structure making ionic and hydrophobic interactions. One region is the fibrinogen recognition exosite and the other, the putative heparin binding site. The lack of inhibition of fibrinogen clotting and platelet activation by the DNA 15-mer with the Arg75-->Glu mutant of thrombin is consistent with the several salt bridges of the DNA in the fibrinogen exosite. The association of DNA with the heparin site of a neighboring molecule appears to simply compensate residual charge. Differences in the 15-mer loop conformations between the complex and NMR solution structures can be attributed to conformational changes upon thrombin binding. Although G-quadruplexes are favored in the presence of monovalent cations, there is no evidence of the latter in the thrombin complex.

    Organizational Affiliation: 

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



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-Thrombin light chainB [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
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-Thrombin heavy chainC [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
GTEx:  ENSG00000180210
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'A [auth D]15N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    0G7
    Query on 0G7
    Download Ideal Coordinates CCD File 
    		 D [auth H]D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide
    C21 H31 Cl N6 O3
    KWPACVJPAFGBEQ-IKGGRYGDSA-N    		 Ligand Interaction
    External Ligand Annotations 
    IDBinding Affinity (Sequence Identity %)
    0G7IC50:  1.5   nM  BindingDB
    Biologically Interesting Molecules (External Reference) 1 Unique
    Entity ID: 4
    IDChainsNameType/Class2D Diagram3D Interactions
    PRD_000021 (0G7)
    Query on PRD_000021    		 D [auth H]D-Phe-Pro-Arg chloromethylketone (PPACK)Peptide-like /  Inhibitor  Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.90 Å
    • R-Value Work: 0.159 
    • R-Value Observed: 0.159 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 56.52α = 90
    b = 77.44β = 90
    c = 99.52γ = 90
    Software Package:
    Software NamePurpose
    X-PLORrefinement

    Structure Validation

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    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1994-06-22
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2011-07-27
      Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
    • Version 1.4: 2013-02-27
      Changes: Other