8TC6: Sequence specific (AATT and TGTCA) orientation of netropsin and ImPyPy molecules at two unique minor groove binding sites within a self-assembled 3D DNA lattice (4x5)

PDB ID: 8TC6Download
MMDB ID: 240286
PDB Deposition Date: 2023/6/29
Updated in MMDB: 2023/12
Experimental Method:
x-ray diffraction
Resolution: 2.45  Å
Source Organism:
Biological Unit for 8TC6: tetrameric; determined by author
Molecular Components in 8TC6
Label Count Molecule
Nucleotides(4 molecules)
1
DNA (5'-d(*gp*ap*gp*cp*ap*gp*ap*cp*cp*tp*gp*ap*cp*gp*ap*tp*gp*tp*cp*ap*c*(nt))-3')
Molecule annotation
1
DNA (5'-d(p*cp*gp*tp*cp*a)-3')
Molecule annotation
1
DNA (5'-d(*tp*cp*gp*tp*gp*ap*cp*ap*t)-3')
Molecule annotation
1
DNA (5'-d(p*gp*gp*tp*cp*tp*gp*c)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (5 molecules)
1
1
NETROPSINNETROPSIN
2
2
N-[5-({5-[(3-{[3-(dimethylamino)propyl]amino}-3-oxopropyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]-1-methyl-1H-imidazole-2-carboxamideN-[5-({5-[(3-{[3-(dimethylamino)propyl]amino}-3-oxopropyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]-1-methyl-1H-imidazole-2-carboxamide
3
2
CACODYLATE IONCACODYLATE ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303