SMTL ID : 4qbr.1 (1 other biounit)

Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ALA- ARG- THR- LYS- GLN- THR- ALA: Histone H3(Non-covalent)

ALA-ARG-THR-LYS-GLN-THR-ALA.1: 19 residues within 4Å: Chain A: D.55, D.57, Y.59, Q.60, S.61, Y.62, G.68, G.69, R.70, E.71, V.72, L.73, M.74, C.75, D.76, A.101, I.102, E.104, W.107 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.72, A:V.72, A:I.102, A:W.107 Hydrogen bonds: A:Q.60, A:Y.62, A:G.69, A:R.70, A:E.71, A:E.71, A:V.72, A:V.72, A:M.74, A:C.75, A:E.104 Water bridges: A:Y.59, A:Y.59 Salt bridges: A:D.76

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.75, C.80, C.109, C.112 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.75, A:C.80, A:C.109, A:C.112 ZN.3: 4 residues within 4Å: Chain A: C.63, C.66, C.85, C.88 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:C.66, A:C.85, A:C.88 ZN.4: 4 residues within 4Å: Chain A: C.20, C.23, C.40, C.43 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.20, A:C.23, A:C.40, A:C.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noh, K. et al., Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs. To be Published

Release Date

2015-05-13

Peptides

DNA (cytosine-5)-methyltransferase 3A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA (cytosine-5)-methyltransferase 3A

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