SMTL ID : 4gus.1

Crystal structure of LSD2-NPAC with H3 in space group P3221

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: I.342, G.343, 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, N.394, Y.533, P.551, V.552, T.580, V.581, P.582, I.591, I.613, W.711, W.716, A.720, Y.721, G.748, E.749, Q.757, T.758, V.759, A.762 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.613, A:I.613, A:W.711, A:A.720 Hydrogen bonds: A:A.347, A:A.367, 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:G.345, A:G.348, A:G.373, A:R.374, A:R.374, A:Y.499, A:Y.533, A:K.615 Salt bridges: A:R.374, A:R.374 pi-Stacking: A:Y.721, A:Y.721

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: K.368, D.369 Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: Q.224, P.225, F.226, Q.228 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: P.81, K.82 Ligand excluded by PLIP IOD.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: E.8, K.9, K.82, I.160 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: M.125 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: W.376, R.388, T.709, R.710, W.711, D.714 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.388, A:R.388, A:R.710, A:D.714, A:D.714 GOL.9: 6 residues within 4Å: Chain A: L.684, Q.685, M.688, R.692, D.702, P.703 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.692

3 x ZN: ZINC ION(Non-covalent)

ZN.10: 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.11: 5 residues within 4Å: Chain A: C.19, C.27, A.28, 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.12: 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

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: A
Putative oxidoreductase GLYR1: B
Histone H3.3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Lysine-specific histone demethylase 1B

Putative oxidoreductase GLYR1

Histone H3.3

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