SMTL ID : 3swr.1

Structure of human DNMT1 (601-1600) in complex with Sinefungin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

monomer

Ligands

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 20 residues within 4Å: Chain A: F.547, S.548, G.549, C.550, G.551, G.552, L.553, E.570, M.571, W.572, D.592, C.593, G.625, P.627, L.649, E.668, N.980, A.981, V.982 Ligands: EDO.23 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.548, A:G.549, A:C.550, A:G.551, A:G.552, A:L.553, A:M.571, A:W.572, A:D.592, A:C.593, A:N.980, A:V.982 Water bridges: A:F.547, A:G.625 pi-Stacking: A:F.547

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: L.25, E.248, R.661, R.691, M.692 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.248, A:M.692 Water bridges: A:E.254, A:R.661, A:R.661 Salt bridges: A:R.661

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 6 residues within 4Å: Chain A: P.584, G.585, S.586, T.587, V.588, Q.611 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.588, A:Q.611 Water bridges: A:R.612 MES.4: 6 residues within 4Å: Chain A: R.180, H.197, L.218, Y.238, Y.267, V.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.180, A:Y.267 Salt bridges: A:H.197

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

EDO.5: 7 residues within 4Å: Chain A: G.707, W.797, F.798, Q.801, L.802, P.985 Ligands: EDO.21 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: F.698, G.699, V.700, L.743, V.745, F.752, V.753, S.754 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: I.333, Y.342, G.460, R.461, N.483, R.758 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: L.728, E.993, L.996 Ligands: EDO.11 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: G.481, P.482, L.992, K.995 Ligands: EDO.11 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: Y.437, H.438, R.770, D.771, S.774, Q.795, S.796 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: P.482, L.992, E.993 Ligands: EDO.8, EDO.9 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: W.270, D.272, Y.275, R.277, E.279, L.728 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: W.270, E.279, S.280, P.282, R.300 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: D.108, D.109, R.671, S.675, S.744, V.745, V.746 Ligands: EDO.17 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: V.366, Y.371, H.374, P.831, D.840 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: P.390, V.735, F.736, C.741, L.759, S.760 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: R.678, S.679, V.746, V.747, D.748 Ligands: EDO.14 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain A: H.121, P.175, L.176, Y.177, L.178, F.199, A.201, D.204 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: L.599, E.604, T.606, N.607 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: W.567, R.612 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: I.441, H.734, F.764, W.797 Ligands: EDO.5, EDO.22 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: N.442, S.478, R.484, W.797 Ligands: EDO.21 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: G.625, P.626, E.668, N.669, R.714, N.980 Ligands: SFG.1 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: V.107, R.713, R.739, A.740 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: C.55, N.931, E.933, R.976 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: G.56, V.57, W.912, L.915, M.935 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: P.831, L.832, A.833 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: T.433, T.766, T.768, D.922 Ligands: EDO.29 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain A: T.433, R.765 Ligands: EDO.28 Ligand excluded by PLIP

4 x ZN: ZINC ION(Non-covalent)

ZN.30: 4 residues within 4Å: Chain A: C.55, C.58, C.61, C.93 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.55, A:C.55, A:C.58, A:C.61, A:C.93 ZN.31: 5 residues within 4Å: Chain A: C.66, G.67, C.69, C.72, C.88 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:C.72, A:C.88 ZN.32: 5 residues within 4Å: Chain A: H.195, C.222, C.295, S.297, C.298 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.195, A:C.222, A:C.295, A:C.298 ZN.33: 4 residues within 4Å: Chain A: C.878, C.880, C.887, H.904 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.878, A:C.880, A:C.887, A:H.904

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hashimoto, H. et al., Structure of human DNMT1 (residues 600-1600) in complex with Sinefungin. To be Published

Release Date

2011-08-10

Peptides

DNA (cytosine-5)-methyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA (cytosine-5)-methyltransferase 1