SMTL ID : 3vxx.1

Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

ACT.1: 2 residues within 4Å: Chain A: E.53, F.55 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.55 ACT.2: 5 residues within 4Å: Chain A: R.17, K.25, F.26, D.27 Chain B: C.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.26 Salt bridges: A:R.17 ACT.3: 5 residues within 4Å: Chain A: V.6, P.7, C.8, G.9, W.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.9 ACT.4: 6 residues within 4Å: Chain A: W.10, P.33, Q.34, N.51, E.53, T.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.34 ACT.8: 3 residues within 4Å: Chain B: T.2, C.3 Chain C: C.13 No protein-ligand interaction detected (PLIP) ACT.9: 3 residues within 4Å: Chain B: C.13 Chain C: T.2, C.3 No protein-ligand interaction detected (PLIP)

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

EDO.5: 5 residues within 4Å: Chain A: Q.16, R.17, L.18 Chain C: C.3, C.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.27 EDO.6: 3 residues within 4Å: Chain A: F.26, V.28 Chain B: A.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.26 Water bridges: A:V.28 EDO.7: 3 residues within 4Å: Chain A: V.65, L.66, P.67 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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