SMTL ID : 6c1t.1

MBD2 in complex with a partially methylated DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: S.40, P.41, S.42, K.44, Y.55 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.40, A:S.42, A:S.42, A:S.42, A:Y.55 Salt bridges: A:K.44

24 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 1 residues within 4Å: Chain A: E.22 Ligand excluded by PLIP UNX.3: 3 residues within 4Å: Chain A: I.24, K.26 Ligands: UNX.12 Ligand excluded by PLIP UNX.4: 7 residues within 4Å: Chain A: R.25, S.27, L.29, S.30, A.31 Chain C: T.6, G.7 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: W.18, L.56 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: F.39, K.45 Chain C: A.4 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: K.49, F.65, D.66, F.67 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: V.60, L.62 Ligand excluded by PLIP UNX.9: 5 residues within 4Å: Chain A: R.25, D.35 Chain B: T.4, A.5 Ligands: UNX.15 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain A: K.44, K.45 Ligand excluded by PLIP UNX.11: 6 residues within 4Å: Chain A: Y.37, R.47 Chain B: C.6, A.7 Chain C: T.6 Ligands: UNX.13 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: V.23, I.24 Ligands: UNX.3 Ligand excluded by PLIP UNX.13: 6 residues within 4Å: Chain A: Y.37, K.45, R.47 Chain C: A.4, G.5 Ligands: UNX.11 Ligand excluded by PLIP UNX.14: 6 residues within 4Å: Chain A: R.47 Chain B: C.8 Chain C: G.3, A.4 Ligands: UNX.16, UNX.20 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain B: A.5 Ligands: UNX.9 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain B: C.8 Ligands: UNX.14, UNX.20 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain B: G.12 Chain C: G.2 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain C: G.11, C.12 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain C: G.7, T.8, A.9 Ligand excluded by PLIP UNX.20: 4 residues within 4Å: Chain B: C.8 Chain C: G.3 Ligands: UNX.14, UNX.16 Ligand excluded by PLIP UNX.21: 4 residues within 4Å: Chain B: T.9 Chain C: A.4, G.5, T.6 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain C: G.3, A.4 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain D: S.40, P.41, S.42, Y.55 Ligand excluded by PLIP UNX.25: 4 residues within 4Å: Chain D: K.49, F.65, D.66, F.67 Ligand excluded by PLIP UNX.26: 3 residues within 4Å: Chain D: K.33, S.34, R.68 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 4 residues within 4Å: Chain C: C.1 Chain D: I.24, R.25, K.26 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.26 Water bridges: D:I.24, D:D.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, K. et al., Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA. J. Biol. Chem. (2018)

Release Date

2018-02-14

Peptides

Methyl-CpG-binding domain protein 2: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

Methyl-CpG-binding domain protein 2

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