SMTL ID : 4xbf.1

Structure of LSD1:CoREST in complex with ssRNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-4-4-mer

Ligands

4 x U- U- A- G- G: RNA (5'-R(*UP*UP*AP*GP*G)-3')(Non-covalent)

U-U-A-G-G.1: 23 residues within 4Å: Chain A: G.109, K.110, G.429, I.445, Y.446, K.447, C.448, D.449 Chain C: R.424, T.426, A.427, V.470, P.471, P.472, P.612, G.613, P.614, S.615 Chain E: I.616, P.617, G.618, A.619, P.620 Protein-ligand interaction information (PLIP) not available U-U-A-G-G.9: 23 residues within 4Å: Chain A: R.424, T.426, A.427, V.470, P.471, P.472, P.612, G.613, P.614, S.615 Chain C: G.109, K.110, G.429, I.445, Y.446, K.447, C.448, D.449 Chain G: I.616, P.617, G.618, A.619, P.620 Protein-ligand interaction information (PLIP) not available U-U-A-G-G.17: 23 residues within 4Å: Chain A: I.616, P.617, G.618, A.619, P.620 Chain E: G.109, K.110, G.429, I.445, Y.446, K.447, C.448, D.449 Chain G: R.424, T.426, A.427, V.470, P.471, P.472, P.612, G.613, P.614, S.615 Protein-ligand interaction information (PLIP) not available U-U-A-G-G.25: 23 residues within 4Å: Chain C: I.616, P.617, G.618, A.619, P.620 Chain E: R.424, T.426, A.427, V.470, P.471, P.472, P.612, G.613, P.614, S.615 Chain G: G.109, K.110, G.429, I.445, Y.446, K.447, C.448, D.449 Protein-ligand interaction information (PLIP) not available

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

FAD.2: 42 residues within 4Å: Chain A: I.114, G.115, S.116, G.117, V.118, S.119, G.120, 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.165, T.418, A.419, V.420, T.454, L.455, P.456, V.459, V.467, L.489, K.491, W.581, W.586, S.590, Y.591, G.630, E.631, A.639, T.640, V.641, H.642, A.644 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.489, A:Y.591 Hydrogen bonds: A:G.117, A:V.118, A:S.119, A:S.119, A:S.119, A:E.138, 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:T.640, A:V.641 Water bridges: A:G.120, A:R.140, A:R.146, A:R.146 Salt bridges: A:R.146, A:R.146 FAD.10: 42 residues within 4Å: Chain C: I.114, G.115, S.116, G.117, V.118, S.119, G.120, 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.165, T.418, A.419, V.420, T.454, L.455, P.456, V.459, V.467, L.489, K.491, W.581, W.586, S.590, Y.591, G.630, E.631, A.639, T.640, V.641, H.642, A.644 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:L.489, C:Y.591 Hydrogen bonds: C:G.117, C:V.118, C:S.119, C:S.119, C:S.119, C:E.138, C:A.139, C:R.140, C:G.144, C:R.146, C:A.161, C:M.162, C:V.163, C:V.163, C:V.420, C:V.420, C:E.631, C:T.640, C:V.641 Water bridges: C:G.120, C:R.140, C:R.146, C:R.146 Salt bridges: C:R.146, C:R.146 FAD.18: 42 residues within 4Å: Chain E: I.114, G.115, S.116, G.117, V.118, S.119, G.120, 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.165, T.418, A.419, V.420, T.454, L.455, P.456, V.459, V.467, L.489, K.491, W.581, W.586, S.590, Y.591, G.630, E.631, A.639, T.640, V.641, H.642, A.644 27 PLIP interactions: 27 interactions with chain E Hydrophobic interactions: E:L.489, E:Y.591 Hydrogen bonds: E:G.117, E:V.118, E:S.119, E:S.119, E:S.119, E:E.138, E:A.139, E:R.140, E:G.144, E:R.146, E:A.161, E:M.162, E:V.163, E:V.163, E:V.420, E:V.420, E:E.631, E:T.640, E:V.641 Water bridges: E:G.120, E:R.140, E:R.146, E:R.146 Salt bridges: E:R.146, E:R.146 FAD.26: 42 residues within 4Å: Chain G: I.114, G.115, S.116, G.117, V.118, S.119, G.120, 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.165, T.418, A.419, V.420, T.454, L.455, P.456, V.459, V.467, L.489, K.491, W.581, W.586, S.590, Y.591, G.630, E.631, A.639, T.640, V.641, H.642, A.644 27 PLIP interactions: 27 interactions with chain G Hydrophobic interactions: G:L.489, G:Y.591 Hydrogen bonds: G:G.117, G:V.118, G:S.119, G:S.119, G:S.119, G:E.138, G:A.139, G:R.140, G:G.144, G:R.146, G:A.161, G:M.162, G:V.163, G:V.163, G:V.420, G:V.420, G:E.631, G:T.640, G:V.641 Water bridges: G:G.120, G:R.140, G:R.146, G:R.146 Salt bridges: G:R.146, G:R.146

20 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain A: R.140, R.142, L.159, S.579, R.580, W.581, D.584 Ligands: SO4.4 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: R.140, D.141, R.142, W.586 Ligands: SO4.3 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: K.204, S.352, R.354 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: S.517, E.520, A.541, I.544, M.545, R.556 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: R.17, T.19, S.20, Q.21 Chain E: S.31 Ligand excluded by PLIP SO4.11: 8 residues within 4Å: Chain C: R.140, R.142, L.159, S.579, R.580, W.581, D.584 Ligands: SO4.12 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain C: R.140, D.141, R.142, W.586 Ligands: SO4.11 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: K.204, S.352, R.354 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain C: S.517, E.520, A.541, I.544, M.545, R.556 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain C: R.17, T.19, S.20, Q.21 Chain G: S.31 Ligand excluded by PLIP SO4.19: 8 residues within 4Å: Chain E: R.140, R.142, L.159, S.579, R.580, W.581, D.584 Ligands: SO4.20 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain E: R.140, D.141, R.142, W.586 Ligands: SO4.19 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain E: K.204, S.352, R.354 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain E: S.517, E.520, A.541, I.544, M.545, R.556 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain A: S.31 Chain E: R.17, T.19, S.20, Q.21 Ligand excluded by PLIP SO4.27: 8 residues within 4Å: Chain G: R.140, R.142, L.159, S.579, R.580, W.581, D.584 Ligands: SO4.28 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain G: R.140, D.141, R.142, W.586 Ligands: SO4.27 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain G: K.204, S.352, R.354 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain G: S.517, E.520, A.541, I.544, M.545, R.556 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain C: S.31 Chain G: R.17, T.19, S.20, Q.21 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: G.239, L.242, E.243, I.246, R.356, D.360, F.363, L.374, T.515, R.518 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.239, A:R.356, A:R.356, A:D.360, A:R.518, A:R.518 GOL.16: 10 residues within 4Å: Chain C: G.239, L.242, E.243, I.246, R.356, D.360, F.363, L.374, T.515, R.518 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.239, C:R.356, C:R.356, C:D.360, C:R.518, C:R.518 GOL.24: 10 residues within 4Å: Chain E: G.239, L.242, E.243, I.246, R.356, D.360, F.363, L.374, T.515, R.518 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.239, E:R.356, E:R.356, E:D.360, E:R.518, E:R.518 GOL.32: 10 residues within 4Å: Chain G: G.239, L.242, E.243, I.246, R.356, D.360, F.363, L.374, T.515, R.518 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:G.239, G:R.356, G:R.356, G:D.360, G:R.518, G:R.518

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirschi, A. et al., G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme. RNA (2016)

Release Date

2016-04-27

Peptides

Lysine-specific histone demethylase 1A: ACEG
REST corepressor 1: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Lysine-specific histone demethylase 1A

REST corepressor 1

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