2I2I | pdb_00002i2i

Crystal structure of the DB293-D(CGCGAATTCGCG)2 complex.

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2006-08-16 Released: 2007-07-31 
  • Deposition Author(s): Lee, M.P.H., Neidle, S.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 
    0.313 (Depositor), 0.283 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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

Literature

Crystal structure of the DB293-D(CGCGAATTCGCG)2 complex.

Lee, M.P.H., Neidle, S.

To be published.

Macromolecule Content 

  • Total Structure Weight: 7.7 kDa 
  • Atom Count: 594 
  • Modeled Residue Count: 24 
  • Deposited Residue Count: 24 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  Sequence
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
MBC

Query on MBC


Download:Ideal Coordinates CCD File
D [auth A]2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-FURYL)-1H-BENZIMIDAZOLE-5-CARBOXIMIDAMIDE
C19 H16 N6 O
LXJNJISEUJIGFP-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: 1.63 Å
  • R-Value Free:  0.313 (Depositor), 0.283 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.176α = 90
b = 39.762β = 90
c = 65.75γ = 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: 2007-07-31
    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