SMTL ID : 6w8v.1

Crystal structure of mouse DNMT1 in complex with ACG DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.12 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 19 residues within 4Å: Chain A: F.419, S.420, G.421, G.423, G.424, L.425, I.441, E.442, M.443, W.444, D.464, C.465, G.497, P.499, L.521, N.851, A.852, V.853 Chain E: C.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: 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.851, A:V.853 pi-Stacking: A:F.419, A:F.419 SAH.4: 20 residues within 4Å: Chain B: F.419, S.420, G.421, G.423, G.424, L.425, I.441, E.442, M.443, W.444, E.463, D.464, C.465, G.497, P.499, L.521, N.851, A.852, V.853 Chain F: C.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:F.419, B:S.420, B:G.423, B:G.424, B:L.425, B:M.443, B:W.444, B:D.464, B:C.465, B:N.851, B:V.853 pi-Stacking: B:F.419, B:F.419

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.750, C.752, C.758, H.775 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.750, A:C.752, A:C.758, A:H.775 ZN.3: 5 residues within 4Å: Chain A: H.67, C.94, C.168, S.170, C.171 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.67, A:C.94, A:C.168, A:C.171 ZN.5: 4 residues within 4Å: Chain B: C.750, C.752, C.758, H.775 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.750, B:C.752, B:C.758, B:H.775 ZN.6: 5 residues within 4Å: Chain B: H.67, C.94, C.168, S.170, C.171 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.67, B:C.94, B:C.168, B:C.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adam, S. et al., DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context. Nat Commun (2020)

Release Date

2020-07-08

Peptides

DNA (cytosine-5)-methyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA (cytosine-5)-methyltransferase 1

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