SMTL ID : 4fwj.3 (2 other biounits)

Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.2: 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.3: 5 residues within 4Å: Chain A: C.39, A.41, 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.6: 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 ZN.7: 4 residues within 4Å: Chain B: C.27, C.32, H.58, 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.8: 6 residues within 4Å: Chain B: C.39, A.41, C.47, A.48, 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

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

FAD.4: 37 residues within 4Å: Chain A: I.362, G.363, A.364, 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, S.570, P.571, V.572, T.600, V.601, P.602, I.611, I.633, W.731, W.736, A.740, Y.741, G.768, E.769, Q.777, T.778, V.779, A.782 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.633, A:I.633, A:W.731, A:A.740 Hydrogen bonds: A:A.367, A:A.387, A:G.393, 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:A.770, A:T.780 Salt bridges: A:R.394, A:R.394 FAD.9: 37 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, L.605, I.611, I.633, K.635, W.731, W.736, A.740, Y.741, G.768, E.769, Q.777, T.778, V.779, A.782 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:R.394, B:I.633, B:K.635, B:W.731, B:A.740 Hydrogen bonds: B:A.367, B:A.387, B:G.393, 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:R.394, B:R.394, B:Y.553, B:A.770 Salt bridges: B:R.394, B:R.394

1 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain A: S.44, E.45, H.77 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 4 residues within 4Å: Chain B: D.450, T.452, I.453, R.456 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.450, B:T.452 Salt bridges: B:R.456

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
B

Lysine-specific histone demethylase 1B

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