SMTL ID : 8fdv.1

LSD1-CoREST in complex N-formyl FAD and SNAG peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PRO- ARG- SER- PHE- LEU- VAL- ARG- LYS- PRO: Zinc finger protein SNAI1(Non-covalent)

PRO-ARG-SER-PHE-LEU-VAL-ARG-LYS-PRO.1: 23 residues within 4Å: Chain A: T.354, Q.377, C.379, L.381, D.394, E.398, N.402, N.554, L.555, F.557, A.558, N.559, W.571, D.572, D.574, D.575, E.578, H.583, L.696, Y.780, A.828, T.829 Ligands: HUF.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.354, A:W.571, A:L.696, A:Y.780, A:T.829 Hydrogen bonds: A:Q.377, A:Q.377, A:N.554, A:N.554, A:N.559, A:D.574 Salt bridges: A:D.394, A:E.398, A:D.572

1 x HUF: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate(Non-covalent)

HUF.2: 36 residues within 4Å: Chain A: G.304, S.305, G.306, V.307, S.308, E.327, A.328, R.329, G.333, G.334, R.335, L.348, G.349, A.350, M.351, V.352, T.607, A.608, V.609, T.643, L.644, P.645, V.648, V.656, L.678, W.770, W.775, S.779, Y.780, G.819, E.820, A.828, T.829, V.830, A.833 Ligands: PRO-ARG-SER-PHE-LEU-VAL-ARG-LYS-PRO.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:R.335 Hydrogen bonds: A:S.305, A:G.306, A:S.308, A:S.308, A:A.328, A:R.329, A:R.335, A:R.335, A:M.351, A:V.352, A:V.352, A:V.609, A:V.609, A:E.820, A:A.828, A:A.828, A:V.830 Salt bridges: A:R.335, A:R.335 pi-Stacking: A:Y.780

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caroli, J. et al., Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1. to be published

Release Date

2024-06-12

Peptides

Lysine-specific histone demethylase 1A: A
REST corepressor 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific histone demethylase 1A

REST corepressor 1

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