1D21

BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Observed: 0.208

Literature

Macromolecules
Sequence Display for 1D21

Classification: DNA

Total Structure Weight: 5282.28

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*(5CM)P*GP*TP*(AS)P*(5CM)P*G)-3') A, B 6 synthetic

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

A, B NOGALAMYCIN
C39 H49 N O16
KGTDRFCXGRULNK-JYOBTZKQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
5CM
Query on 5CM
A, B DNA LINKING C10 H16 N3 O7 P DC
AS
Query on AS
A, B DNA LINKING C10 H14 N5 O5 P S DA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Observed: 0.208
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 26.31 α = 90.00
b = 26.31 β = 90.00
c = 100.25 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1990-08-08
  • Released Date: 1991-07-15
  • Deposition author(s): Gao, Y.-G., Liaw, Y.-C., Robinson, H., Wang, A.H.-J.

Revision History

  • 2008-05-22
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance
  • 2011-08-24
    Type: Atomic model, Derived calculations