SMTL ID : 4gu1.3 (2 other biounits)

Crystal structure of LSD2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: I.350, G.351, G.353, P.354, A.355, L.373, E.374, A.375, K.376, G.380, G.381, R.382, R.396, G.397, A.398, Q.399, I.400, Y.541, P.559, V.560, T.588, V.589, P.590, I.599, I.621, W.719, W.724, A.728, G.756, E.757, Q.765, T.766, V.767, A.770 Chain B: L.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:R.382, A:I.621, A:W.719, A:A.728 Hydrogen bonds: A:A.355, A:A.375, A:K.376, A:R.382, A:R.382, A:Q.399, A:I.400, A:I.400, A:Y.541, A:V.560, A:V.560, A:E.757, A:Q.765, A:V.767 Salt bridges: A:R.382, A:R.382 FAD.8: 34 residues within 4Å: Chain A: L.2 Chain B: I.350, G.351, A.352, G.353, P.354, A.355, L.373, E.374, A.375, K.376, G.381, R.382, R.396, G.397, A.398, Q.399, I.400, Y.541, P.559, V.560, T.588, V.589, P.590, W.719, W.724, A.728, Y.729, G.756, E.757, Q.765, T.766, V.767, A.770 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:R.382, B:W.719, B:A.728 Hydrogen bonds: B:A.352, B:A.355, B:A.375, B:K.376, B:G.381, B:R.382, B:Q.399, B:I.400, B:I.400, B:V.560, B:V.560, B:E.757, B:Q.765, B:V.767 Salt bridges: B:R.382, B:R.382 pi-Stacking: B:Y.729

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

CL.2: 5 residues within 4Å: Chain A: E.16, W.44, Y.45, H.46, K.90 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.127, K.292, H.296 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: E.16, W.44, Y.45, H.46, K.90 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: K.127, K.292, H.296 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: Y.565, G.567, Q.749 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.749 NA.11: 4 residues within 4Å: Chain B: Y.565, G.567, D.568, Q.749 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.567

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.15, C.20, H.46, H.52 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.15, A:C.20, A:H.46, A:H.52 ZN.6: 5 residues within 4Å: Chain A: C.27, A.29, C.35, C.54, C.57 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.27, A:C.35, A:C.54, A:C.57 ZN.7: 4 residues within 4Å: Chain A: C.104, C.109, C.131, C.147 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.104, A:C.109, A:C.131, A:C.147 ZN.12: 4 residues within 4Å: Chain B: C.15, C.20, H.46, H.52 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.15, B:C.20, B:H.46, B:H.52 ZN.13: 6 residues within 4Å: Chain B: C.27, A.29, C.35, A.36, C.54, C.57 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.27, B:C.35, B:C.54, B:C.57 ZN.14: 4 residues within 4Å: Chain B: C.104, C.109, C.131, C.147 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.104, B:C.109, B:C.131, B:C.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fang, R. et al., LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol.Cell (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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