3QLP

X-ray structure of the complex between human alpha thrombin and a modified thrombin binding aptamer (mTBA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Thrombin-aptamer recognition: a revealed ambiguity.

Russo Krauss, I.Merlino, A.Giancola, C.Randazzo, A.Mazzarella, L.Sica, F.

(2011) Nucleic Acids Res. 39: 7858-7867

  • DOI: 10.1093/nar/gkr522
  • Also Cited By: 4I7Y, 4DII, 4DIH

  • PubMed Abstract: 
  • Aptamers are structured oligonucleotides that recognize molecular targets and can function as direct protein inhibitors. The best-known example is the thrombin-binding aptamer, TBA, a single-stranded 15-mer DNA that inhibits the activity of thrombin, ...

    Aptamers are structured oligonucleotides that recognize molecular targets and can function as direct protein inhibitors. The best-known example is the thrombin-binding aptamer, TBA, a single-stranded 15-mer DNA that inhibits the activity of thrombin, the key enzyme of coagulation cascade. TBA folds as a G-quadruplex structure, as proved by its NMR structure. The X-ray structure of the complex between TBA and human α-thrombin was solved at 2.9-Å resolution, but did not provide details of the aptamer conformation and the interactions with the protein molecule. TBA is rapidly processed by nucleases. To improve the properties of TBA, a number of modified analogs have been produced. In particular, a modified TBA containing a 5'-5' polarity inversion site, mTBA, has higher stability and higher affinity toward thrombin with respect to TBA, although it has a lower inhibitory activity. We present the crystal structure of the thrombin-mTBA complex at 2.15-Å resolution; the resulting model eventually provides a clear picture of thrombin-aptamers interaction, and also highlights the structural bases of the different properties of TBA and mTBA. Our findings open the way for a rational design of modified aptamers with improved potency as anticoagulant drugs.


    Organizational Affiliation

    Università di Napoli Federico II, Via Cintia, Napoli, Italia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsLengthOrganism
modified thrombin binding DNA aptamerD15N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
0G6
Query on 0G6

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Download CCD File 
H
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
PPACK
C21 H34 Cl N6 O3
DVFLYEYCMMLBTQ-VSZNYVQBSA-O
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020
HD-Phe-Pro-Arg-CH2ClPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.208α = 90.00
b = 110.574β = 90.00
c = 120.916γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Other