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SMTL ID : 6r1u.1

Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

FAD.1:

35 residues within 4Å:

Chain K: 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

22 PLIP interactions:

22 interactions with chain K

Hydrophobic interactions: K:R.374, K:I.613, K:I.613, K:W.711, K:A.720
Hydrogen bonds: K:A.344, K:A.347, K:A.367, K:R.374, K:Q.391, K:I.392, K:I.392, K:N.394, K:V.552, K:V.552, K:E.749, K:Q.757, K:V.759
Salt bridges: K:R.374, K:R.374
pi-Stacking: K:Y.721, K:Y.721

3 x ZN: ZINC ION(Non-covalent)

ZN.2:	4 residues within 4Å: Chain K: C.7, C.12, H.38, H.44 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.7, K:C.12, K:H.38, K:H.44
ZN.3:	6 residues within 4Å: Chain K: C.19, S.22, C.27, A.28, C.46, C.49 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.19, K:C.27, K:C.46, K:C.49
ZN.4:	4 residues within 4Å: Chain K: C.96, C.101, C.123, C.139 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.96, K:C.101, K:C.123, K: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

Histone H3.2: AE
Histone H4: BF
Histone H2A: CG
Histone H2B 1.1: DH
Lysine-specific histone demethylase 1B: K
Putative oxidoreductase GLYR1: L
Histone H3: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

K
K

L
L

M
M

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3.2

Histone H4

Histone H2A

Histone H2B 1.1

Lysine-specific histone demethylase 1B

Putative oxidoreductase GLYR1

Histone H3

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