8CMN
18mer DNA mimic Foldamer with an aliphatic linker in complex with Sac7d wild protein
This is a non-PDB format compatible entry.
Summary for 8CMN
| Entry DOI | 10.2210/pdb8cmn/pdb |
| Descriptor | DNA-binding protein 7d, N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide (3 entities in total) |
| Functional Keywords | foldamer, dna mimic, dna binding protein, histone |
| Biological source | Sulfolobus acidocaldarius DSM 639 More |
| Total number of polymer chains | 3 |
| Total formula weight | 12700.35 |
| Authors | Deepak, D.,Corvaglia, V.,Wu, J.,Huc, I. (deposition date: 2023-02-20, release date: 2023-07-19, Last modification date: 2025-02-26) |
| Primary citation | Deepak, D.,Wu, J.,Corvaglia, V.,Allmendinger, L.,Scheckenbach, M.,Tinnefeld, P.,Huc, I. DNA Mimic Foldamer Recognition of a Chromosomal Protein. Angew.Chem.Int.Ed.Engl., 64:e202422958-e202422958, 2025 Cited by PubMed Abstract: Helical aromatic oligoamide foldamers bearing anionic side chains that mimic the overall shape and charge surface distribution of DNA were synthesized. Their interactions with chromosomal protein Sac7d, a non-sequence-selective DNA-binder that kinks DNA, were investigated by Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC), Circular Dichroism spectroscopy (CD), melting curve analysis, Atomic Force Microscopy (AFM), and Nuclear Magnetic Resonance (NMR), as well as by single crystal X-ray crystallography. The foldamers were shown to bind to Sac7d better than a DNA duplex of comparable length. The interaction is diastereoselective and takes place at the DNA binding site. Crystallography revealed that the DNA mimic foldamers have a binding mode of their own and that they can bind to Sac7d without being kinked. PubMed: 39714421DOI: 10.1002/anie.202422958 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.65 Å) |
Structure validation
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