1HAP

COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTTGGTGTGGTTGG (BASED ON X-RAY MODEL OF DNA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

An ambiguous structure of a DNA 15-mer thrombin complex.

Padmanabhan, K., Tulinsky, A.

(1996) Acta Crystallogr D Biol Crystallogr 52: 272-282

  • DOI: 10.1107/S0907444995013977
  • Primary Citation of Related Structures:  
    1HAP, 1HAO

  • PubMed Abstract: 

    • The structure of a complex between thrombin and a GGTTGGTGTGGTTGG DNA 15-mer has been analyzed crystallographically. The solution NMR structure of the 15-mer has two stacked G-quartets similar to that found in the previous X-ray structure determination o ...

    The structure of a complex between thrombin and a GGTTGGTGTGGTTGG DNA 15-mer has been analyzed crystallographically. The solution NMR structure of the 15-mer has two stacked G-quartets similar to that found in the previous X-ray structure determination of the 15-mer-thrombin complex [Padmanabhan, Padmanabhan, Ferrara, Sadler & Tulinsky (1993). J. Biol. Chem. 268, 17651-17654]; the strand polarity, however, is reversed from that of the crystallographic structure. The structure of the complex here has been redetermined with better diffraction data confirming the previous crystallographic structure but also indicating that the NMR solution structure fits equally well. Both 15-mer complex structures refined to an R value of about 0.16 presenting a disconcerting ambiguity. Since the two 15-mer structures associate with thrombin in different ways (through the TGT loop in the X-ray and TT loop in the NMR model), other independent lines of physical or chemical evidence are required to resolve the ambiguity.

    Related Citations: 
    • 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
    Organizational Affiliation: 

    Department of Chemistry, Michigan State University, East Lansing 48824, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chain L36Homo 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
GTEx:  ENSG00000180210
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chain H259Homo 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
GTEx:  ENSG00000180210
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'D15N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    0G6
    Query on 0G6
    Download Ideal Coordinates CCD File 
    H
    		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    		HD-Phe-Pro-Arg-CH2ClPeptide-like /  Inhibitor

    --

    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Observed: 0.161 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 58.28α = 90
    b = 77.61β = 90
    c = 100.02γ = 90
    Software Package:
    Software NamePurpose
    NUCLINrefinement
    PROLSQrefinement

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1996-04-03
      Type: Initial release
    • Version 1.1: 2008-05-22
      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