SMTL ID : 7kz1.1

Human MBD4 glycosylase domain bound to DNA containing an abasic site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: E.66, V.67 No protein-ligand interaction detected (PLIP)

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

EDO.2: 1 residues within 4Å: Chain A: W.105 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.105, A:K.106, A:Y.122

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: I.109, L.111, I.114 Chain B: A.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.114, A:I.114

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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