SMTL ID : 5ciy.1

Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: F.18, A.19, G.20, L.21, G.22, G.23, F.24, N.39, E.40, W.41, D.42, D.60, I.61, G.78, P.80, L.100, Y.285, N.304, S.305, V.306 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:F.18, A:L.21, A:G.22, A:G.23, A:W.41, A:D.60, A:I.61, A:Y.285 Water bridges: A:F.18, A:F.24, A:F.24, A:D.42, A:N.304, A:N.304 pi-Stacking: A:F.18, A:F.18, A:W.41, A:W.41

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

SO4.2: 2 residues within 4Å: Chain A: P.198, D.199 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.199 Water bridges: A:L.197, A:D.199, A:S.200, A:N.268, A:N.268 SO4.3: 1 residues within 4Å: Chain A: K.290 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.290, A:K.290 Salt bridges: A:K.290 SO4.4: 3 residues within 4Å: Chain A: P.286, D.287, S.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.287, A:S.288 Water bridges: A:S.288, A:S.288 SO4.5: 3 residues within 4Å: Chain A: I.219, E.220, Q.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.220, A:Q.221 SO4.6: 2 residues within 4Å: Chain A: K.114, R.172 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.114, A:R.172, A:R.172, A:R.172 Salt bridges: A:K.114, A:R.172 SO4.7: 4 residues within 4Å: Chain A: L.196, L.197, P.198, R.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.196 Salt bridges: A:R.281 SO4.8: 4 residues within 4Å: Chain A: K.137, N.141, S.146, F.147 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.141, A:F.147 Water bridges: A:K.137, A:K.137 Salt bridges: A:K.137 SO4.9: 1 residues within 4Å: Chain A: W.41 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.41, A:D.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rondelet, G. et al., Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B. J.Struct.Biol. (2016)

Release Date

2016-03-30

Peptides

Modification methylase HhaI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Modification methylase HhaI

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