6X9K: Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A

PDB ID: 6X9KDownload
MMDB ID: 203940
PDB Deposition Date: 2020/6/2
Updated in MMDB: 2023/10
Experimental Method:
x-ray diffraction
Resolution: 2.65  Å
Source Organism:
Similar Structures:
Biological Unit for 6X9K: trimeric; determined by author and by software (PISA)
Molecular Components in 6X9K
Label Count Molecule
Protein (1 molecule)
1
DNA (Cytosine-5)-methyltransferase 1
(Gene symbol: DNMT1)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*gp*ap*gp*gp*cp*(5cm)p*gp*cp*cp*tp*gp*c)-3')
Molecule annotation
1
DNA (5'-d(*gp*cp*ap*gp*g)-r(p*(pyo))-d(p*gp*gp*cp*cp*tp*c)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (12 molecules)
1
2
ZINC IONZINC ION
2
9
1,2-ETHANEDIOL1,2-ETHANEDIOL
3
1
(2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide(2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide
* 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