SMTL ID : 8bpc.1

Cryo-EM structure of the human SIN3B histone deacetylase core complex with SAHA at 2.8 Angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x SHH: OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE(Non-covalent)

SHH.1: 13 residues within 4Å: Chain A: F.440 Chain B: H.29, P.30, D.100, H.141, H.142, G.150, F.151, D.177, H.179, D.265, Y.304 Ligands: ZN.2 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.30, B:F.151, B:F.151, B:F.151, B:F.151, A:F.440 Hydrogen bonds: B:D.100, B:H.142, B:Y.304

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain B: D.177, I.178, H.179, D.265 Ligands: SHH.1 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.177, B:D.177, B:H.179, B:D.265 ZN.5: 4 residues within 4Å: Chain C: C.289, C.292, C.315, H.318 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.289, C:C.292, C:C.315, C:H.318 ZN.6: 4 residues within 4Å: Chain C: C.274, C.277, H.297, C.300 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.274, C:C.277, C:H.297, C:C.300

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain B: D.175, D.177, H.179, S.198, F.199, H.200 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.175, B:D.177, B:H.179, B:F.199 CA.4: 4 residues within 4Å: Chain B: F.188, T.191, V.194, Y.223 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.188, B:T.191, B:V.194, B:Y.223, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, M.S.M. et al., Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex. Nat Commun (2023)

Release Date

2023-05-10

Peptides

Isoform 2 of Paired amphipathic helix protein Sin3b: A
Histone deacetylase 2: B
PHD finger protein 12: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Isoform 2 of Paired amphipathic helix protein Sin3b

Histone deacetylase 2

PHD finger protein 12

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