SMTL ID : 7xi9.1

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.1126, C.1128, C.1135, H.1152 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1126, A:C.1128, A:C.1135, A:H.1152 ZN.2: 4 residues within 4Å: Chain A: H.443, C.470, C.543, C.546 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.443, A:C.470, A:C.543, A:C.546 ZN.3: 5 residues within 4Å: Chain A: C.303, G.304, C.306, C.309, C.341 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.303, A:C.306, A:C.309, A:C.341 ZN.4: 5 residues within 4Å: Chain A: C.314, C.317, C.320, C.336, Q.337 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.314, A:C.317, A:C.320, A:C.336

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

SAH.5: 21 residues within 4Å: Chain A: F.795, S.796, G.797, G.799, G.800, L.801, I.817, E.818, M.819, W.820, E.839, D.840, C.841, G.873, P.875, L.897, E.916, N.1228, A.1229, V.1230 Chain C: C.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.799, A:G.800, A:L.801, A:M.819, A:W.820, A:D.840, A:D.840, A:C.841, A:N.1228, A:V.1230 Water bridges: A:C.798, A:G.873, A:K.894, A:N.1228 pi-Stacking: A:F.795, A:F.795

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kikuchi, A. et al., Structural basis for activation of DNMT1. Nat Commun (2022)

Release Date

2022-11-30

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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