SMTL ID : 4fwe.2 (1 other biounit)

Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.27, C.32, H.58, S.60, H.64 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.27, A:C.32, A:H.58, A:H.64 ZN.2: 5 residues within 4Å: Chain A: C.39, S.42, C.47, C.66, C.69 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.39, A:C.47, A:C.66, A:C.69 ZN.3: 4 residues within 4Å: Chain A: C.116, C.121, C.143, C.159 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.116, A:C.121, A:C.143, A:C.159 ZN.6: 5 residues within 4Å: Chain B: C.27, C.32, H.58, S.60, H.64 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.27, B:C.32, B:H.58, B:H.64 ZN.7: 5 residues within 4Å: Chain B: C.39, S.42, C.47, C.66, C.69 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.39, B:C.47, B:C.66, B:C.69 ZN.8: 4 residues within 4Å: Chain B: C.116, C.121, C.143, C.159 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.116, B:C.121, B:C.143, B:C.159

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

FAD.4: 38 residues within 4Å: Chain A: I.362, G.363, G.365, P.366, A.367, L.385, E.386, A.387, K.388, G.392, G.393, R.394, R.408, G.409, A.410, Q.411, I.412, Y.553, P.571, V.572, T.600, V.601, P.602, I.611, I.633, K.635, W.731, W.736, I.737, M.739, A.740, Y.741, G.768, E.769, Q.777, T.778, V.779, A.782 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:R.394, A:I.633, A:I.633, A:K.635, A:W.731, A:A.740, A:Y.741 Hydrogen bonds: A:A.367, A:A.387, A:R.394, A:Q.411, A:I.412, A:I.412, A:Y.553, A:V.572, A:V.572, A:E.769, A:Q.777, A:V.779 Water bridges: A:G.365, A:G.368, A:G.393, A:R.394, A:R.394, A:N.414, A:K.635, A:T.780 Salt bridges: A:R.394, A:R.394 FAD.9: 38 residues within 4Å: Chain B: I.362, G.363, G.365, P.366, A.367, L.385, E.386, A.387, K.388, G.392, G.393, R.394, R.408, G.409, A.410, Q.411, I.412, Y.553, P.571, V.572, T.600, V.601, P.602, I.611, I.633, K.635, W.731, W.736, I.737, M.739, A.740, Y.741, G.768, E.769, Q.777, T.778, V.779, A.782 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:R.394, B:I.633, B:I.633, B:K.635, B:W.731, B:A.740, B:Y.741 Hydrogen bonds: B:A.367, B:A.387, B:R.394, B:Q.411, B:I.412, B:I.412, B:V.572, B:V.572, B:E.769, B:Q.777, B:V.779 Water bridges: B:G.365, B:G.368, B:G.393, B:R.394, B:R.394, B:N.414, B:Y.553, B:K.635 Salt bridges: B:R.394, B:R.394

2 x FLC: CITRATE ANION(Non-covalent)

FLC.5: 6 residues within 4Å: Chain A: Y.247, C.252, G.253, F.539, A.540, H.774 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.253, A:A.540 Water bridges: A:Y.247, A:K.254, A:C.257 Salt bridges: A:H.774, A:H.774 FLC.10: 6 residues within 4Å: Chain B: Y.247, C.252, G.253, F.539, A.540, H.774 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.247, B:G.253, B:A.540 Water bridges: B:Y.247, B:K.254, B:C.257 Salt bridges: B:H.774, B:H.774

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Q. et al., Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b. Cell Res. (2013)

Release Date

2013-01-16

Peptides

Lysine-specific histone demethylase 1B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lysine-specific histone demethylase 1B

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