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SMTL ID : 7e8d.1

NSD2 E1099K mutant bound to nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1:	5 residues within 4Å: Chain K: C.172, C.219, C.221, C.226, S.227 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.172, K:C.219, K:C.221, K:C.226
ZN.2:	5 residues within 4Å: Chain K: C.44, C.46, C.54, C.60 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.44, K:C.46, K:C.54, K:C.60
ZN.3:	5 residues within 4Å: Chain K: C.54, C.69, C.74, C.80 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.54, K:C.69, K:C.74, K:C.80

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.4:

15 residues within 4Å:

Chain E: M.36
Chain K: G.100, K.101, W.103, T.143, H.144, F.145, Y.146, R.166, F.167, N.169, H.170, Y.207, R.220, C.221

15 PLIP interactions:

15 interactions with chain K

Hydrophobic interactions: K:Y.146, K:Y.207
Hydrogen bonds: K:W.103, K:T.143, K:H.144, K:F.145, K:R.166, K:N.169, K:N.169, K:H.170, K:H.170, K:Y.207, K:Y.207, K:R.220
Salt bridges: K:H.144

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sato, K. et al., Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2. Nat Commun (2021)

Release Date

2021-11-10

Peptides

Histone H3.1: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B type 1-J: DH
Histone-lysine N-methyltransferase NSD2: K

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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3.1

Histone H4

Histone H2A type 1

Toggle Identical (CG)

Histone H2B type 1-J

Histone-lysine N-methyltransferase NSD2

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