1DA5 | pdb_00001da5

Solution structure of a DNA Duplex containing the CIS-PT(NH3)2[D(-GTG-)-N7-(G)-N7(G)N7(G)]Adduct as determined with high field NMR And molecular mechanics/dynamics

• PDB DOI: https://doi.org/10.2210/pdb1DA5/pdb
• NAKB: 1DA5

• Classification: DNA
• Mutation(s): No 


• Deposited: 1993-01-13 Released: 1994-01-31 
• Deposition Author(s): Van Garderen, C.J., Van Houte, L.P.A.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 2 

Literature

The solution structure of a DNA duplex containing the cis-Pt(NH3)2[d(-GTG-)-N7(G),N7(G)] adduct, as determined with high-field NMR and molecular mechanics/dynamics.

van Garderen, C.J., van Houte, L.P.

(1994) Eur J Biochem 225: 1169-1179

• PubMed: 7957208 
• Primary Citation Related Structures: 
  1DA4, 1DA5


• PubMed Abstract: 
  

  The solution structure of the cis-Pt-GTG adduct in the double-stranded oligomer d(CTCTAGTGCTCAC).td(GTGAGCACTAGAG) was studied with high-resolution NMR techniques. For model building, the distance information obtained from two-dimensional NOE experiments was used in molecular mechanic computations and molecular dynamic structure refinements. The structural distortion upon platination appears to be restricted to the base pairs Pt-G6.C21 and T7.A20; Pt-G8.C19 forms a normal Watson-Crick base pair. T7 is positioned in the minor groove and stacks with the highly propeller-twisted Pt-G6. There is no hydrogen bonding between T7 and A20. The complementary strand is undistorted; A20 stacks with its flanking cytidines (C19 and C21) as in regular B-DNA. The duplex is locally unwound (from base pair A5.T22 to G8.C19: 19 degrees) and is slightly kinked (20 degrees) at the platination site. The platinum coordination distorts the DNA structure at the 5' side of the platinated-GTG-sequence and changes the minor groove face.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.24 kDa 
• Atom Count: 536 
• Modeled Residue Count: 26 
• Deposited Residue Count: 26 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*CP*TP*AP*GP*TP*GP*CP*TP*CP*AP*C)-3')	A	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*GP*AP*GP*CP*AP*CP*TP*AP*GP*AP*G)-3')	B	13	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPT	C [auth A]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 2 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Van Garderen, C.J., Van Houte, L.P.A.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-04-10
  Changes: Data collection, Database references, Derived calculations, Other