SMTL ID : 6z2j.1

The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 4 residues within 4Å: Chain A: K.31, R.270, R.306 Chain F: Y.157 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F Salt bridges: A:K.31, A:R.270, A:R.306 Hydrogen bonds: F:Y.157 IHP.5: 5 residues within 4Å: Chain B: G.27, K.31, R.270, R.306 Chain E: Y.157 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:Y.157 Salt bridges: B:K.31, B:K.31, B:R.270

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.176, I.177, H.178, D.264, G.301 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.176, A:D.176, A:H.178, A:D.264 ZN.6: 5 residues within 4Å: Chain B: D.176, I.177, H.178, D.264, G.301 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.176, B:D.176, B:H.178, B:D.264

4 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: D.174, D.176, H.178, H.179, G.180, S.197, F.198, H.199 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.174, A:D.174, A:D.176, A:S.197, A:F.198 K.4: 5 residues within 4Å: Chain A: F.187, T.190, V.193, Y.222, A.223 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.187, A:T.190, A:V.193, A:Y.222 K.7: 8 residues within 4Å: Chain B: D.174, D.176, H.178, H.179, G.180, S.197, F.198, H.199 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.174, B:D.174, B:D.176, B:S.197, B:F.198 K.8: 5 residues within 4Å: Chain B: F.187, T.190, V.193, Y.222, A.223 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:F.187, B:T.190, B:V.193, B:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Turnbull, R.E. et al., The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure. Nat Commun (2020)

Release Date

2020-07-08

Peptides

Histone deacetylase 1: AB
Deoxynucleotidyltransferase terminal-interacting protein 1: CD
Mitotic deacetylase-associated SANT domain protein: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
A

D
B

E
F

F
D

Histone deacetylase 1

Deoxynucleotidyltransferase terminal-interacting protein 1

Mitotic deacetylase-associated SANT domain protein

Related Entries With Identical Sequence