5ODM

NtiPr polyamide in complex with 5'CGATGTACTACG3


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 2000 
  • Conformers Submitted: 10 
  • Selection Criteria: clustering 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides.

Padroni, G.Parkinson, J.A.Fox, K.R.Burley, G.A.

(2018) Nucleic Acids Res. 46: 42-53

  • DOI: 10.1093/nar/gkx1211
  • Primary Citation of Related Structures:  5ODF, 5OE1, 5OCZ

  • PubMed Abstract: 
  • This manuscript reports the molecular basis for double-stranded DNA (dsDNA) binding of hairpin polyamides incorporating a 5-alkyl thiazole (Nt) unit. Hairpin polyamides containing an N-terminal Nt unit induce higher melting stabilisation of target ds ...

    This manuscript reports the molecular basis for double-stranded DNA (dsDNA) binding of hairpin polyamides incorporating a 5-alkyl thiazole (Nt) unit. Hairpin polyamides containing an N-terminal Nt unit induce higher melting stabilisation of target dsDNA sequences relative to an archetypical hairpin polyamide incorporating an N-terminal imidazole (Im) unit. However, modification of the N-terminus from Im to Nt-building blocks results in an increase in dsDNA binding affinity but lower G-selectivity. A general G-selectivity trend is observed for Nt-containing polyamide analogues. G-selectivity increases as the steric bulk in the Nt 5-position increases. Solution-based NMR structural studies reveal differences in the modulation of the target DNA duplex of Nt-containing hairpin polyamides relative to the Im-containing archetype. A structural hallmark of an Nt polyamide•dsDNA complex is a more significant degree of major groove compression of the target dsDNA sequence relative to the Im-containing hairpin polyamide.


    Organizational Affiliation

    Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')A,B12Homo sapiens
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9T8
Query on 9T8

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Download CCD File 
A
3-(3-azaniumylpropanoylamino)propyl-dimethyl-azanium
C8 H21 N3 O
CKBSAZMXMFCAGN-UHFFFAOYSA-P
 Ligand Interaction
IMT
Query on IMT

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A
4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID
C5 H7 N3 O2
PPQDQYBXCYQCNH-UHFFFAOYSA-N
 Ligand Interaction
9U2
Query on 9U2

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Download CCD File 
A
5-propan-2-yl-1,3-thiazole-4-carbaldehyde
C7 H9 N O S
ZNCIEQFZRKIVOL-UHFFFAOYSA-N
 Ligand Interaction
PYB
Query on PYB

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Download CCD File 
A
4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID
C6 H8 N2 O2
MUEOQEUSJMFYHV-UHFFFAOYSA-N
 Ligand Interaction
ABU
Query on ABU

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Download CCD File 
A
GAMMA-AMINO-BUTANOIC ACID
GAMMA(AMINO)-BUTYRIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DCZ
Query on DCZ
A, B
DNA OH 5 prime terminusC9 H13 N3 O4

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 2000 
  • Conformers Submitted: 10 
  • Selection Criteria: clustering 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Database references