› 1dsi

Solution NMR

Solution structure of a duocarmycin sa-indole-alkylated dna dupleX

Released:
DOI: 10.2210/pdb1dsi/pdb
PDB entry 1dsi coloured by chain, ensemble of 20 models, front view.
PDB entry 1dsi coloured by chain, ensemble of 20 models, side view.
PDB entry 1dsi coloured by chain, ensemble of 20 models, top view.
Source organism: Synthetic construct
Primary publication:
Binding-Induced Activation of DNA Alkylation by Duocarmycin SA: Insights from the Structure of an Indole Derivative-DNA Adduct
Schnell JR, Ketchem RR, Boger DL, Chazin WJ
J. Am. Chem. Soc. 121 5645-5652 (1999)

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113710 (preferred)
Entry contents:
2 distinct DNA molecules
Macromolecules (2 distinct):
DNA (5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3') Chain: A
Molecule details ›
Chain: A
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: Synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand DSI 1 x DSI
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: NAB TO GENERATE A FAMILY OF CONFOMRERS THAT SAMPLE A WIDE RANGE OF CONFORMATIONAL SPACE. RESTRAINED MOLECULAR DYNAMICS TO GENERATE A RANGE OF STARTING STRUCTURES FOR DSI. PAIRS OF DNA AND DSI STRUCTURES WERE THEN DOCKED AND ITERATIVELY REFINED BY A SERIES OF RESTRAINED MOLECULAR DYNAMICS CALCULATIONS.
Expression system: Not provided

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