1D35

FACILE FORMATION OF A CROSSLINKED ADDUCT BETWEEN DNA AND THE DAUNORUBICIN DERIVATIVE MAR70 MEDIATED BY FORMALDEHYDE: MOLECULAR STRUCTURE OF THE MAR70-D(CGTNACG) COVALENT ADDUC

Structural Biology Knowledgebase: 1D35 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Observed: 0.174

Literature

Macromolecules
Sequence Display for 1D35

Classification: DNA

Total Structure Weight: 2520.25

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*TP*(A40)P*CP*G)-3') A 6 synthetic

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

A 4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN
MAR70;DAUNOMYCIN DERIVATIVE (Synonym)
C33 H39 N O13
QTGKDZKONUUXOU-NIGIIATCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
A40
Query on A40
A DNA LINKING C11 H17 N6 O6 P DA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Observed: 0.174
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 28.12 α = 90.00
b = 28.12 β = 90.00
c = 52.98 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1991-04-23
  • Released Date: 1992-04-15
  • Deposition author(s): Gao, Y.-G., Liaw, Y.-C., Li, Y.-K., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4