SMTL ID : 4qbs.1

Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

ALA-ARG-TPO-LYS-GLN-THR-ALA.1: 17 residues within 4Å: Chain A: D.56, D.58, Y.60, Q.61, S.62, Y.63, G.70, R.71, R.72, V.73, L.74, M.75, C.84, A.102, I.103, E.105, W.108 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.73, A:V.73, A:I.103, A:W.108 Hydrogen bonds: A:D.56, A:Q.61, A:R.71, A:V.73, A:V.73, A:M.75, A:E.105 Water bridges: A:D.58, A:Y.60, A:R.71, A:M.75 Salt bridges: A:R.72

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.76, C.81, C.110, C.113 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.76, A:C.81, A:C.110, A:C.113 ZN.3: 4 residues within 4Å: Chain A: C.64, C.67, C.86, C.89 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.67, A:C.86, A:C.89 ZN.4: 4 residues within 4Å: Chain A: C.21, C.24, C.41, C.44 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.21, A:C.24, A:C.41, A:C.44

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

SO4.5: 3 residues within 4Å: Chain A: G.114, H.115, K.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.115, A:K.116 Salt bridges: A:H.115

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