SMTL ID : 7sfg.1

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.750, C.752, C.759, H.776 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.750, A:C.752, A:C.759, A:H.776 ZN.2: 4 residues within 4Å: Chain A: H.67, C.94, C.167, C.170 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.67, A:C.94, A:C.167, A:C.170

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 20 residues within 4Å: Chain A: F.419, S.420, G.421, C.422, G.423, G.424, L.425, E.442, M.443, W.444, E.463, D.464, C.465, G.497, P.499, L.521, N.852, A.853, V.854 Chain C: U.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:F.419, A:S.420, A:C.422, A:G.423, A:G.424, A:L.425, A:M.443, A:W.444, A:D.464, A:C.465, A:N.852, A:V.854 Water bridges: A:S.426, A:G.497 pi-Stacking: A:F.419

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: G.579, W.669, F.670, Q.673, L.674, P.857 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.578, A:H.606

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: I.205, Y.214, G.332, R.333, N.355, R.630 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.333, A:N.355, A:R.630 Water bridges: A:N.355 EDO.6: 6 residues within 4Å: Chain A: R.333, C.334, T.335, P.354, N.355 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.335, A:T.335, A:N.355 EDO.7: 5 residues within 4Å: Chain A: W.117, E.120, R.533, R.563, M.564 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.120, A:R.533, A:R.533 EDO.8: 3 residues within 4Å: Chain A: P.456, S.458, T.459 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.459 Water bridges: A:S.458, A:V.460 EDO.9: 6 residues within 4Å: Chain A: S.646, L.648, W.793, H.815, E.817, Q.818 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.646, A:E.817, A:Q.818 EDO.10: 3 residues within 4Å: Chain A: F.840, G.841, K.846 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.841, A:K.846, A:K.846

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors. Structure (2022)

Release Date

2022-03-30

Peptides

DNA (cytosine-5)-methyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA (cytosine-5)-methyltransferase 1

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