SMTL ID : 6r25.1

Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-2-2-2-2-mer

Ligands

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

FAD.1: 35 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, Y.533, P.551, V.552, T.580, V.581, P.582, I.613, W.711, W.716, A.720, Y.721, G.748, E.749, Q.757, T.758, V.759, A.762 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:R.374, A:I.613, A:I.613, A:W.711, A:A.720 Hydrogen bonds: A:A.344, A:A.347, A:A.367, A:R.374, A:Q.391, A:I.392, A:I.392, A:N.394, A:V.552, A:V.552, A:E.749, A:Q.757, A:Q.757, A:V.759 Water bridges: A:G.345, A:G.348, A:E.366, A:E.366, A:R.374, A:R.374, A:Y.533, A:K.615 Salt bridges: A:R.374, A:R.374 pi-Stacking: A:Y.721

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.7, C.12, H.38, 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: 6 residues within 4Å: Chain A: C.19, S.22, 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.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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marabelli, C. et al., A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex. Cell Rep (2019)

Release Date

2019-04-24

Peptides

Lysine-specific histone demethylase 1B: A
NPAC: B
Histone H3: C
Histone H3: DH
H4: EI
Histone H2A: FJ
H2B: GK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
A

H
E

E
B

I
F

F
C

J
G

G
D

K
H

Lysine-specific histone demethylase 1B

NPAC

Histone H3

Histone H3

H4

Histone H2A

H2B

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