SMTL ID : 7kz0.1

Human MBD4 glycosylase domain bound to DNA containing substrate analog 2'-deoxy-pseudouridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: T.45, L.46, H.48, K.52, L.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.45, A:K.52, A:K.52 Water bridges: A:H.48 GOL.3: 1 residues within 4Å: Chain A: E.83 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.83, A:R.86 GOL.4: 4 residues within 4Å: Chain B: G.8 Chain C: T.3, G.4, C.5 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: I.126, L.128, I.131 Chain B: A.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.126, A:L.128, A:I.131, H2O.6, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pidugu, L.S. et al., Structural Insights into the Mechanism of Base Excision by MBD4. J.Mol.Biol. (2021)

Release Date

2021-11-10

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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