SMTL ID : 5h6q.1

Crystal structure of LSD1-CoREST in complex with peptide 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: G.245, E.249, I.252, R.362, F.369, L.380, R.524 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.362, A:R.362, A:R.524, A:R.524 GOL.2: 4 residues within 4Å: Chain A: K.210, S.358, R.360, D.361 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.210, A:S.358, A:S.358 GOL.3: 4 residues within 4Å: Chain A: R.18, I.640, Y.643, R.656 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.18 GOL.4: 6 residues within 4Å: Chain A: R.146, R.148, S.585, R.586, W.587, D.590 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.146, A:R.148, A:R.586 Water bridges: A:R.148

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.5: 38 residues within 4Å: Chain A: G.121, S.122, G.123, V.124, S.125, L.143, E.144, A.145, R.146, G.150, G.151, R.152, V.153, L.165, G.166, A.167, M.168, V.169, T.424, A.425, V.426, T.460, L.461, P.462, V.473, L.495, K.497, W.587, W.592, S.596, Y.597, G.636, E.637, A.645, T.646, V.647, A.650 Chain C: M.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.495 Hydrogen bonds: A:S.122, A:G.123, A:S.125, A:S.125, A:A.145, A:R.146, A:R.146, A:G.150, A:R.152, A:V.153, A:A.167, A:M.168, A:V.169, A:V.169, A:V.426, A:V.426, A:E.637, A:V.647 Water bridges: A:R.152, A:R.152 Salt bridges: A:R.152, A:R.152 pi-Stacking: A:Y.597

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amano, Y. et al., Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1. Bioorg. Med. Chem. (2017)

Release Date

2017-04-12

Peptides

Lysine-specific histone demethylase 1A: A
REST corepressor 1: B
peptide SRTMQTARKSTGGKAPRKQLK: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Lysine-specific histone demethylase 1A

REST corepressor 1

peptide SRTMQTARKSTGGKAPRKQLK

Related Entries With Identical Sequence