SMTL ID : 7ao9.1

Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-2-mer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 8 residues within 4Å: Chain B: K.305, Y.327, Y.328, K.331 Chain C: G.27, K.31, R.270, I.305 15 PLIP interactions: 6 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:G.27, B:Y.327, B:Y.327, B:Y.328 Salt bridges: C:K.31, C:K.31, C:K.31, C:R.270, C:R.270, B:K.305, B:K.305, B:K.305, B:K.331, B:K.331, B:K.331 IHP.5: 8 residues within 4Å: Chain D: K.305, Y.327, Y.328, K.331 Chain E: G.27, K.31, R.270, I.305 14 PLIP interactions: 8 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:Y.327, D:Y.336, E:G.27 Salt bridges: D:K.305, D:K.305, D:K.305, D:K.331, D:K.331, D:K.331, E:K.31, E:K.31, E:K.31, E:R.270, E:R.270

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain C: D.176, I.177, H.178, D.264 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.176, C:D.176, C:H.178, C:D.264 ZN.6: 4 residues within 4Å: Chain E: D.176, I.177, H.178, D.264 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.176, E:D.176, E:H.178, E:D.264

4 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain C: D.174, I.175, D.176, H.178, S.197, F.198, H.199 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.174, C:D.176, C:S.197 K.4: 5 residues within 4Å: Chain C: F.187, T.190, V.193, G.219, Y.222 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:F.187 K.7: 7 residues within 4Å: Chain E: D.174, I.175, D.176, H.178, S.197, F.198, H.199 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.174, E:D.176, E:S.197 K.8: 5 residues within 4Å: Chain E: F.187, T.190, V.193, G.219, Y.222 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:F.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Millard, C.J. et al., The topology of chromatin-binding domains in the NuRD deacetylase complex. Nucleic Acids Res. (2020)

Release Date

2020-11-11

Peptides

Methyl-CpG-binding domain protein 2: A
Metastasis-associated protein MTA1: BD
Histone deacetylase 1: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

D
A

C
E

E
B

Methyl-CpG-binding domain protein 2

Metastasis-associated protein MTA1

Histone deacetylase 1

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