SMTL ID : 3vxv.1

Crystal structure of methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 1 residues within 4Å: Chain A: E.53 No protein-ligand interaction detected (PLIP) ACT.2: 6 residues within 4Å: Chain A: W.10, P.33, Q.34, Y.47, N.51, E.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.34 ACT.8: 3 residues within 4Å: Chain B: C.9, G.10 Ligands: EDO.6 No protein-ligand interaction detected (PLIP)

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

EDO.3: 5 residues within 4Å: Chain A: Q.16, R.17, L.18 Chain C: C.3, T.4 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: G.9, W.10, E.11, I.31, S.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.11, A:I.31 EDO.5: 3 residues within 4Å: Chain A: C.8, G.9, W.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.9, A:W.10 EDO.6: 3 residues within 4Å: Chain A: K.37, F.38 Ligands: ACT.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.43, A:S.43 Water bridges: A:K.37, A:K.37 EDO.7: 3 residues within 4Å: Chain A: V.65, L.66, P.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.68 EDO.9: 3 residues within 4Å: Chain B: C.13 Chain C: T.2, C.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otani, J. et al., Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4. J.Biol.Chem. (2013)

Release Date

2013-01-16

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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