SMTL ID : 3a1b.1

Crystal structure of the DNMT3A ADD domain in complex with histone H3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.39, C.42, C.59, C.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.39, A:C.42, A:C.59, A:C.62 ZN.2: 4 residues within 4Å: Chain A: C.82, C.85, C.104, C.107 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.82, A:C.85, A:C.104, A:C.107 ZN.3: 5 residues within 4Å: Chain A: C.94, N.96, C.99, C.128, C.131 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.94, A:C.99, A:C.128, A:C.131

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

EDO.4: 10 residues within 4Å: Chain A: F.66, C.69, A.70, Q.79, Y.81, C.82, T.83, C.86, R.101 Ligands: EDO.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.79, A:Q.79, A:C.82, A:R.101 Water bridges: A:Y.81 EDO.5: 7 residues within 4Å: Chain A: E.36, V.47, L.49, E.50, G.56, G.57, R.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.56, A:G.56, A:R.143, A:R.143 EDO.6: 4 residues within 4Å: Chain A: A.70, Y.71, Y.73 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.70 EDO.7: 5 residues within 4Å: Chain A: W.126, N.127, C.128, Y.129, Y.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.123, A:C.128 Water bridges: A:N.127 EDO.8: 3 residues within 4Å: Chain A: E.68, Y.71, Q.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.72 EDO.9: 6 residues within 4Å: Chain A: G.88, R.89, E.90, C.104, V.105, E.106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.89, A:E.90, A:V.105, A:E.106 Water bridges: A:G.88, A:E.106 EDO.10: 7 residues within 4Å: Chain A: F.66, A.70, Q.79, R.101, L.150 Ligands: EDO.4, EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.101, A:R.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otani, J. et al., Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. Embo Rep. (2009)

Release Date

2009-11-10

Peptides

DNA (cytosine-5)-methyltransferase 3A, Histone H3.1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA (cytosine-5)-methyltransferase 3A, Histone H3.1