SMTL ID : 4gu0.1 (1 other biounit)

Crystal structure of LSD2 with H3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-1-mer

Ligands

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

FAD.1: 34 residues within 4Å: Chain A: I.342, G.343, A.344, G.345, P.346, A.347, L.365, E.366, A.367, K.368, G.372, G.373, R.374, R.388, G.389, A.390, Q.391, I.392, P.551, V.552, T.580, V.581, P.582, K.615, W.711, W.716, A.720, Y.721, G.748, E.749, Q.757, T.758, V.759, A.762 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:K.615, A:W.711 Hydrogen bonds: A:A.344, A:A.347, A:A.367, A:K.368, A:R.374, A:Q.391, A:I.392, A:I.392, A:V.552, A:V.552, A:E.749, A:Q.757, A:V.759 Water bridges: A:A.750 Salt bridges: A:R.374, A:R.374 pi-Stacking: A:W.716, A:Y.721 FAD.5: 35 residues within 4Å: Chain B: I.342, G.343, A.344, G.345, P.346, A.347, L.365, E.366, A.367, K.368, G.372, G.373, R.374, R.388, G.389, A.390, Q.391, I.392, P.551, V.552, T.580, V.581, P.582, I.591, K.615, W.711, W.716, A.720, Y.721, G.748, E.749, Q.757, T.758, V.759, A.762 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:W.711 Hydrogen bonds: B:A.344, B:A.347, B:A.367, B:R.374, B:Q.391, B:I.392, B:I.392, B:Y.533, B:V.552, B:V.552, B:E.749, B:Q.757, B:V.759 Water bridges: B:A.750, B:T.760 Salt bridges: B:R.374, B:R.374

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.7, C.12, H.38, S.40, H.44 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:C.12, A:H.38, A:H.44 ZN.3: 4 residues within 4Å: Chain A: C.19, C.27, C.46, C.49 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.19, A:C.27, A:C.46, A:C.49 ZN.4: 4 residues within 4Å: Chain A: C.96, C.101, C.123, C.139 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.96, A:C.101, A:C.123, A:C.139 ZN.6: 4 residues within 4Å: Chain B: C.7, C.12, H.38, H.44 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.7, B:C.12, B:H.38, B:H.44 ZN.7: 5 residues within 4Å: Chain B: C.19, S.22, C.27, C.46, C.49 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.19, B:C.27, B:C.46, B:C.49 ZN.8: 4 residues within 4Å: Chain B: C.96, C.101, C.123, C.139 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.96, B:C.101, B:C.123, B:C.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, F. et al., Structural insight into substrate recognition by histone demethylase LSD2/KDM1b. Cell Res. (2013)

Release Date

2013-02-13

Peptides

Lysine-specific histone demethylase 1B: AB
Histone H3.3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

Lysine-specific histone demethylase 1B

Histone H3.3

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