2NLM | pdb_00002nlm

Crystal structure of the DB 911- D(CGCGAATTCGCG)2 complex at 2.05 A resolution.

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2006-10-20 Released: 2007-10-30 
  • Deposition Author(s): Lee, M.P.H., Neidle, S.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.329 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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


Literature

Crystal structure of the DB 911 - D(CGCGAATTCGCG)2 complex at 2.05 A resolution.

Lee, M.P.H., Neidle, S.

To be published.

Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
A, B
12N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DB9
Query on DB9
Download Ideal Coordinates CCD File 
D [auth B]2-{4'-[AMINO(IMINO)METHYL]BIPHENYL-3-YL}-1H-BENZIMIDAZOLE-6-CARBOXIMIDAMIDE
C21 H18 N6
LRMPNDUSMWYCMH-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.329 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.726α = 90
b = 40.065β = 90
c = 65.556γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description