SMTL ID : 2iw5.1

Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-mer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: I.114, G.115, S.116, G.117, V.118, S.119, L.137, E.138, A.139, R.140, G.144, G.145, R.146, V.147, L.159, G.160, A.161, M.162, V.163, T.418, A.419, V.420, T.454, L.455, P.456, V.467, L.489, K.491, W.581, W.586, S.590, Y.591, G.630, E.631, A.639, T.640, V.641, A.644 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:L.489, A:W.581 Hydrogen bonds: A:S.116, A:G.117, A:S.119, A:S.119, A:S.119, A:A.139, A:R.140, A:G.144, A:R.146, A:A.161, A:M.162, A:V.163, A:V.163, A:V.420, A:V.420, A:E.631, A:A.639, A:V.641 Water bridges: A:V.118, A:V.118, A:G.120, A:R.146, A:T.165, A:K.491, A:H.632 Salt bridges: A:R.146, A:R.146 pi-Stacking: A:Y.591

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: W.581, D.584 Ligands: CL.7 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: S.579, R.580 Ligands: CL.2 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: G.239, I.246, R.356, L.374, R.518 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.356, A:R.356, A:R.518, A:R.518 GOL.4: 3 residues within 4Å: Chain A: Q.188, N.365, L.523 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.365

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, M. et al., Structural Basis for Corest-Dependent Demethylation of Nucleosomes by the Human Lsd1 Histone Demethylase. Mol.Cell (2006)

Release Date

2006-08-09

Peptides

LYSINE-SPECIFIC HISTONE DEMETHYLASE 1: A
REST COREPRESSOR 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LYSINE-SPECIFIC HISTONE DEMETHYLASE 1

REST COREPRESSOR 1

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