SMTL ID : 4qbq.1

Crystal structure of DNMT3a ADD domain bound to H3 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

ALA-ARG-THR-LYS-GLN-THR-ALA-ARG.1: 17 residues within 4Å: Chain A: E.72 Chain B: D.56, D.58, Y.60, Q.61, S.62, G.69, G.70, R.71, E.72, V.73, L.74, M.75, A.102, I.103, E.105, W.108 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.73, B:V.73, B:I.103, B:W.108 Hydrogen bonds: B:D.56, B:D.58, B:G.70, B:R.71, B:V.73, B:V.73, B:M.75, B:E.105 Water bridges: B:W.108 Salt bridges: A:E.72

6 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 ZN.5: 4 residues within 4Å: Chain B: C.76, C.81, C.110, C.113 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.76, B:C.81, B:C.110, B:C.113 ZN.6: 4 residues within 4Å: Chain B: C.64, C.67, C.86, C.89 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.67, B:C.86, B:C.89 ZN.7: 4 residues within 4Å: Chain B: C.21, C.24, C.41, C.44 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.21, B:C.24, B:C.41, B:C.44

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

DNA (cytosine-5)-methyltransferase 3A