SMTL ID : 4kum.1

Structure of LSD1-CoREST-Tetrahydrofolate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 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, W.581, W.586, S.590, Y.591, G.630, E.631, A.639, T.640, V.641, A.644 Ligands: THG.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.489 Hydrogen bonds: A:S.116, A:G.117, A:S.119, A:S.119, A:S.119, A:A.139, A:R.140, 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.454, A:H.632 Salt bridges: A:R.146, A:R.146 pi-Stacking: A:Y.591

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: G.239, E.243, I.246, R.356, F.363, R.518 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.356, A:R.356, A:R.518, A:R.518

1 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)

THG.3: 11 residues within 4Å: Chain A: V.163, Q.188, F.368, A.369, E.389, H.394, W.525, Y.591, A.639, T.640 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.368 Hydrogen bonds: A:Q.188, A:A.369, A:Y.591 Salt bridges: A:E.389, A:H.394, A:H.394

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

CL.4: 2 residues within 4Å: Chain A: R.140, R.142 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luka, Z. et al., Crystal structure of the histone lysine specific demethylase LSD1 complexed with tetrahydrofolate. Protein Sci. (2014)

Release Date

2014-05-07

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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