SMTL ID : 6ryu.1

Nucleosome-CHD4 complex structure (two CHD4 copies)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 19 residues within 4Å: Chain K: T.728, L.729, H.730, M.756, G.757, G.759, K.760, T.761, V.762, N.792, E.796, W.800, E.877, L.1134, N.1137, R.1162, R.1165, I.1166 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:T.728, K:G.757, K:K.760, K:K.760, K:T.761, K:T.761, K:T.761, K:V.762, K:N.792, K:E.796, K:N.1137, K:R.1162, K:R.1162, K:R.1165, K:R.1165 Salt bridges: K:R.1165 ANP.5: 19 residues within 4Å: Chain L: T.728, L.729, H.730, M.756, G.757, G.759, K.760, T.761, V.762, N.792, E.796, W.800, E.877, L.1134, N.1137, R.1162, R.1165, I.1166 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:T.728, L:G.757, L:K.760, L:K.760, L:T.761, L:T.761, L:T.761, L:V.762, L:N.792, L:E.796, L:E.877, L:N.1137, L:R.1162, L:R.1162, L:R.1165, L:R.1165 Salt bridges: L:R.1165

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain K: T.761, D.876, E.877 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.876 MG.6: 4 residues within 4Å: Chain L: T.761, D.876, E.877 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.876

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain K: C.455, C.458, H.475, C.478 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.455, K:C.458, K:C.478 ZN.4: 5 residues within 4Å: Chain K: C.467, C.470, S.472, C.493, C.496 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.467, K:C.470, K:C.493, K:C.496 ZN.7: 4 residues within 4Å: Chain L: C.455, C.458, H.475, C.478 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.455, L:C.458, L:C.478 ZN.8: 5 residues within 4Å: Chain L: C.467, C.470, S.472, C.493, C.496 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.467, L:C.470, L:C.493, L:C.496

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farnung, L. et al., Nucleosome-CHD4 chromatin remodeller structure maps human disease mutations. Elife (2020)

Release Date

2020-07-15

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
Chromodomain-helicase-DNA-binding protein 4,CHD4,Chromodomain-helicase-DNA-binding protein 4: KL

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
W

L
V

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Chromodomain-helicase-DNA-binding protein 4,CHD4,Chromodomain-helicase-DNA-binding protein 4

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