SMTL ID : 4ew0.1

mouse MBD4 glycosylase domain in complex with a G:5hmU (5-hydroxymethyluracil) mismatch

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: K.105, Y.106, D.109, E.125, N.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.109, A:D.109, A:E.125, A:N.126, A:N.126 EDO.2: 1 residues within 4Å: Chain A: W.94 No protein-ligand interaction detected (PLIP) EDO.3: 5 residues within 4Å: Chain A: R.8, N.12, L.13, V.14, I.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.8, A:R.8

1 x NI: NICKEL (II) ION(Non-covalent)

NI.4: 4 residues within 4Å: Chain A: I.98, L.100, I.103 Chain C: T.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.98, A:L.100, A:I.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hashimoto, H. et al., Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Nucleic Acids Res. (2012)

Release Date

2012-07-11

Peptides

Methyl-CpG-binding domain protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methyl-CpG-binding domain protein 4

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