SMTL ID : 8voj.1

The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain C: D.176, H.178, D.264, G.301 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.176, C:D.176, C:H.178, C:D.264

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 16 residues within 4Å: Chain B: H.291, R.313, W.315 Chain C: Y.23, Q.26, G.27, H.28, K.31, R.270, I.305, R.306, Y.336 Chain D: K.128, Y.149, Y.150, K.153 15 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B, 5 interactions with chain D Hydrogen bonds: C:G.27, C:R.270, B:R.313, B:R.313, D:Y.150 Salt bridges: C:K.31, C:K.31, C:R.270, C:R.306, B:H.291, B:R.313, D:K.128, D:K.128, D:K.153, D:K.153

1 x 01: (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine

01.3: 16 residues within 4Å: Chain B: I.310, P.311, R.312, D.333, R.334, L.335, K.354, L.356 Chain C: E.98, D.99, G.149, F.150, H.178, F.205, L.271, Y.303 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:E.98, C:D.99, C:F.205, B:I.310, B:L.335, B:L.335 Hydrogen bonds: B:R.312, B:D.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeo, M.J.R. et al., UM171 glues asymmetric CRL3-HDAC1/2 assembly to degrade CoREST corepressors. Nature (2025)

Release Date

2024-12-04

Peptides

Isoform 2 of Kelch repeat and BTB domain-containing protein 4: AB
Histone deacetylase 1: C
REST corepressor 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isoform 2 of Kelch repeat and BTB domain-containing protein 4

Histone deacetylase 1

REST corepressor 1

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