1MK6

SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE

Structural Biology Knowledgebase: 1MK6 SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20
  • Conformers Submitted: 1
  • Selection Criteria: Final Calculated Structure Is Being Submitted. Back Calculated Structure Is in Agreement with Noesy Data. the Calculation Was Performed in Presence of Solvent and Counterions. Solvent and Counterion Co Ordinates Are Not Being Reported Only the Duplex Dna. Before Solvating and Addition of Counter Ions 20 Final Structures Were Calculated Using Xplor. the Final Averaged Energy Minimized Structure Was Solvated and the Counter Ions Were Added to It. Then Md Was Ran For 1.4 Ns Time Scale to Obtain Final Structure.

Literature

Macromolecules
Sequence Display for 1MK6

Classification: DNA

Total Structure Weight: 6441.39

Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*CP*AP*TP*CP*(X)P*AP*TP*CP*T)-3' A 10 synthetic
5'-D(*AP*GP*AP*TP*AP*GP*AP*TP*GP*T)-3' B 10 synthetic

Small Molecules
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
X
Query on X
A DNA LINKING C27 H27 N5 O14 P DG

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20
  • Conformers Submitted: 1
  • Selection Criteria: Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and counterions. Solvent, and Counterion co-ordinates are NOT being reported, only the Duplex DNA. Before Solvating and Addition of Counter IONS, 20 final structures were calculated using XPLOR. The final averaged energy minimized structure was solvated, and the counter Ions were added to it. Then MD was ran for 1.4 ns time scale to obtain final structure.

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2002-08-28
  • Released Date: 2002-10-16
  • Deposition author(s): Giri, I., Johnston, D.S., Stone, M.P.

Revision History

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