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SMTL ID : 6pa7.1

The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

CL.1:	2 residues within 4Å: Chain A: P.121, K.122 Ligand excluded by PLIP
CL.2:	5 residues within 4Å: Chain C: G.46, A.47 Chain D: T.88, S.89 Chain I: T.122 Ligand excluded by PLIP
CL.3:	3 residues within 4Å: Chain G: G.46 Chain H: T.88, S.89 Ligand excluded by PLIP

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4:	15 residues within 4Å: Chain K: F.417, D.418, S.440, E.441, V.442, C.443, D.463, V.464, G.484, P.486, L.507, E.533, R.668, S.669, W.670 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:I.420, K:V.442, K:D.463, K:D.463, K:V.464, K:R.668, K:R.668, K:R.668, K:W.670, K:W.670
SAH.5:	15 residues within 4Å: Chain M: F.417, D.418, S.440, E.441, V.442, C.443, D.463, V.464, G.484, P.486, L.507, E.533, R.668, S.669, W.670 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:I.420, M:V.442, M:D.463, M:D.463, M:V.464, M:R.668, M:R.668, M:R.668, M:W.670, M:W.670

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Xu, T.H. et al., Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Nature (2020)

Release Date

2020-06-17

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
DNA (cytosine-5)-methyltransferase 3A: KM
DNA (cytosine-5)-methyltransferase 3B: LN

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

M
P

L
N

N
S

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 type 1

Histone H2B 1.1

DNA (cytosine-5)-methyltransferase 3A

Toggle Identical (KM)

DNA (cytosine-5)-methyltransferase 3B

Toggle Identical (LN)

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