SMTL ID : 6z2k.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.140, D.176, I.177, H.178, D.264, G.301, Y.303 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.176, A:D.176, A:H.178, A:D.264 ZN.5: 7 residues within 4Å: Chain B: H.140, D.176, I.177, H.178, D.264, G.301, Y.303 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.176, B:D.176, B:H.178, B:D.264 ZN.8: 7 residues within 4Å: Chain C: H.140, D.176, I.177, H.178, D.264, G.301, Y.303 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.176, C:D.176, C:H.178, C:D.264 ZN.11: 7 residues within 4Å: Chain D: H.140, D.176, I.177, H.178, D.264, G.301, Y.303 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.176, D:D.176, D:H.178, D:D.264

8 x K: POTASSIUM ION(Non-covalent)

K.2: 8 residues within 4Å: Chain A: D.174, D.176, H.178, H.179, G.180, S.197, F.198, H.199 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.174, A:D.176, A:S.197, A:F.198 K.3: 9 residues within 4Å: Chain A: F.187, Y.188, T.190, V.193, M.194, T.195, G.219, 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.6: 8 residues within 4Å: Chain B: D.174, D.176, H.178, H.179, G.180, S.197, F.198, H.199 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.174, B:D.176, B:S.197, B:F.198 K.7: 9 residues within 4Å: Chain B: F.187, Y.188, T.190, V.193, M.194, T.195, G.219, 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 K.9: 8 residues within 4Å: Chain C: D.174, D.176, H.178, H.179, G.180, S.197, F.198, H.199 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.174, C:D.176, C:S.197, C:F.198 K.10: 9 residues within 4Å: Chain C: F.187, Y.188, T.190, V.193, M.194, T.195, G.219, Y.222, A.223 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:F.187, C:T.190, C:V.193, C:Y.222 K.12: 8 residues within 4Å: Chain D: D.174, D.176, H.178, H.179, G.180, S.197, F.198, H.199 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.174, D:D.176, D:S.197, D:F.198 K.13: 9 residues within 4Å: Chain D: F.187, Y.188, T.190, V.193, M.194, T.195, G.219, Y.222, A.223 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:F.187, D:T.190, D:V.193, D:Y.222

4 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.4: 8 residues within 4Å: Chain B: G.27, K.31, I.305 Chain I: Y.157, Y.158, K.161 Chain K: K.125, K.129 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain K, 1 interactions with chain I Hydrogen bonds: B:G.27 Salt bridges: B:K.31, K:K.125, K:K.129, I:K.161 IHP.14: 7 residues within 4Å: Chain C: G.27, R.270 Chain I: K.125, K.129 Chain K: Y.157, Y.158, K.161 7 PLIP interactions: 2 interactions with chain I, 4 interactions with chain K, 1 interactions with chain C Salt bridges: I:K.125, I:K.129, K:K.161, K:K.161, K:K.161, C:R.270 Hydrogen bonds: K:Y.157 IHP.15: 8 residues within 4Å: Chain D: G.27, H.28, K.31, I.305 Chain J: K.125, K.129 Chain L: Y.158, K.161 8 PLIP interactions: 3 interactions with chain D, 1 interactions with chain L, 4 interactions with chain J Hydrogen bonds: D:G.27 Salt bridges: D:K.31, D:K.31, L:K.161, J:K.125, J:K.125, J:K.129, J:K.129 IHP.16: 8 residues within 4Å: Chain A: Q.26, G.27, K.31 Chain J: Y.157, Y.158, K.161 Chain L: K.125, K.129 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain A, 2 interactions with chain J Salt bridges: L:K.125, L:K.129, J:K.161 Hydrogen bonds: A:G.27, J:Y.157

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: ABCD
Deoxynucleotidyltransferase terminal-interacting protein 1: EFGH
Mitotic deacetylase-associated SANT domain protein: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
K

D
I

E
A

F
B

G
G

H
H

I
F

J
D

K
L

L
J

Histone deacetylase 1

Deoxynucleotidyltransferase terminal-interacting protein 1

Mitotic deacetylase-associated SANT domain protein

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