SMTL ID : 8ba5.1

Crystal structure of the DNMT3A ADD domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: D.59, S.65, Y.66 Ligands: MG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.59 EDO.2: 7 residues within 4Å: Chain A: F.51, C.54, A.55, Y.66, C.67, T.68, C.71 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.51, A:Y.66 Water bridges: A:Y.56, A:Q.57, A:T.68, A:R.86

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.24, C.27, C.44, C.47 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.24, A:C.27, A:C.44, A:C.47 ZN.4: 4 residues within 4Å: Chain A: C.67, C.70, C.89, C.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.89, A:C.92 ZN.5: 4 residues within 4Å: Chain A: C.79, C.84, C.113, C.116 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.79, A:C.84, A:C.113, A:C.116

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 1 residues within 4Å: Ligands: EDO.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunert, S. et al., The MECP2-TRD domain interacts with the DNMT3A-ADD domain at the H3-tail binding site. Protein Sci. (2023)

Release Date

2022-11-23

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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