SMTL ID : 5gut.1

The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: F.418, S.419, G.420, C.421, G.422, G.423, L.424, E.441, M.442, W.443, E.462, D.463, C.464, G.496, P.498, L.520, N.850, A.851, V.852 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:F.418, A:S.419, A:G.420, A:C.421, A:G.422, A:G.423, A:L.424, A:M.442, A:D.463, A:C.464, A:V.852 Water bridges: A:S.425, A:G.496, A:N.850 pi-Stacking: A:F.418

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.66, C.93, C.167, C.170 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.66, A:C.93, A:C.167, A:C.170 ZN.3: 4 residues within 4Å: Chain A: C.749, C.751, C.757, H.774 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.749, A:C.751, A:C.757, A:H.774

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

SO4.4: 5 residues within 4Å: Chain A: Q.573, T.582, R.583, R.584, T.797 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.584, A:R.584, A:T.797 Water bridges: A:T.582, A:R.584, A:R.584, A:T.797 Salt bridges: A:R.584 SO4.5: 3 residues within 4Å: Chain A: Q.679, R.683, S.834 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.679 Salt bridges: A:R.683 SO4.6: 3 residues within 4Å: Chain A: Q.716, H.726, K.727 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.716, A:K.727 Salt bridges: A:H.726 SO4.7: 4 residues within 4Å: Chain A: N.223, D.319, E.320, E.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.223, A:E.321, A:E.321 SO4.8: 5 residues within 4Å: Chain A: R.451, T.457, T.458, V.459, Q.482 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.459, A:Q.482 Salt bridges: A:R.451 SO4.9: 5 residues within 4Å: Chain A: N.509, R.511, T.512, K.515, R.548 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.509, A:T.512 Salt bridges: A:R.511, A:K.515, A:R.548 SO4.10: 3 residues within 4Å: Chain A: H.301, R.302, F.369 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.301, A:R.302 SO4.11: 3 residues within 4Å: Chain A: L.693, F.764, S.765 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.765 Water bridges: A:R.762, A:T.766 SO4.12: 3 residues within 4Å: Chain A: A.219, F.220, T.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.221 SO4.13: 5 residues within 4Å: Chain A: Y.143, N.144, Q.145, E.146, R.172 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.143, A:Q.145, A:Q.145, A:E.146 Water bridges: A:G.91 Salt bridges: A:R.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, F. et al., Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1. ACS Chem. Biol. (2018)

Release Date

2017-09-06

Peptides

DNA (cytosine-5)-methyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA (cytosine-5)-methyltransferase 1