1QDA

Crystal structure of epidoxorubicin-formaldehyde virtual crosslink of DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 1QDA

Classification: DNA

Total Structure Weight: 2368.76

Macromolecule Entities
Molecule Chains Length Organism Details
5' -D(CP*GP*CP*(G49)P*CP*GP)-3' A 6 synthetic DOXORUBICIN COVALENTLY ATTACHED TO N2(G4) VIA METHYLENE BRIDGE

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DM6
Query on DM6

A 4'-EPIDOXORUBICIN
4'-EPIADRIAMYCIN (Synonym)
C27 H30 N O11
AOJJSUZBOXZQNB-VTZDEGQISA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
G49
Query on G49
A DNA LINKING C11 H16 N5 O7 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.205
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 28.11 α = 90.00
b = 28.11 β = 90.00
c = 52.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-05-17
  • Released Date: 1999-09-15
  • Deposition author(s): Podell, E.R., Harrington, D.J., Taatjes, D.J., Koch, T.H.

Revision History

  • Version 1_0: 1999-09-15

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2014-03-12

    Type: Database references

  • Version 1_4: 2017-10-04

    Type: Refinement description