101D

REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON DENSITY MAP INTERPRETATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation.

Goodsell, D.S.Kopka, M.L.Dickerson, R.E.

(1995) Biochemistry 34: 4983-4993


  • PubMed Abstract: 
  • The X-ray crystal structure of the complex of the B-DNA dodecamer CGCGAATTCGCG with the antitumor drug netropsin has been reexamined to locate the drug accurately for computer-based drug design. The optimum solution is with the drug centered in the A ...

    The X-ray crystal structure of the complex of the B-DNA dodecamer CGCGAATTCGCG with the antitumor drug netropsin has been reexamined to locate the drug accurately for computer-based drug design. The optimum solution is with the drug centered in the AATT region of the minor groove, making three good bifurcated hydrogen bonds with adenine N3 and thymine O2 atoms along the floor of the groove. Pyrrole rings of netropsin are packed against the C2 positions of adenines, leaving no room for the amine group of guanine and, hence, providing a structural rationale for the A.T specificity of netropsin. An alternative positioning in which the drug is shifted along the minor groove by ca. one-half base pair step is rejected on the basis of free R factor calculations and the appearance of the original drug-free difference maps. Final omit maps, although of more pleasing appearance, are not a dependable means of discriminating between right and wrong structures. The shifted alternative drug position ignores potential hydrogen bonding along the floor of the groove, provides no explanation for netropsin's observed A.T specificity, and is contradicted by NMR results [Patel, D. J. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 6424].


    Related Citations: 
    • Binding of an Antitumor Drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G
      Kopka, M.L.,Yoon, C.,Goodsell, D.S.,Pjura, P.,Dickerson, R.E.
      (1985) J.Mol.Biol. 183: 553


    Organizational Affiliation

    Department of Chemistry & Biochemistry, University of California, Los Angeles 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')A,B12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NT
Query on NT

Download SDF File 
Download CCD File 
B
NETROPSIN
C18 H26 N10 O3
IDBIFFKSXLYUOT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBR
Query on CBR
A, B
DNA LINKINGC9 H13 Br N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 24.270α = 90.00
b = 39.620β = 90.00
c = 63.570γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance