SMTL ID : 8f86.1

SIRT6 bound to an H3K9Ac nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZSL: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name)(Covalent)

ZSL.1: 22 residues within 4Å: Chain A: K.9 Chain K: G.52, A.53, G.54, T.57, D.63, F.64, R.65, G.66, Q.113, H.133, W.188, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:A.53, K:G.54, K:T.57, K:D.63, K:D.63, K:R.65, K:R.65, K:G.66, K:T.215, K:S.216, K:L.241, K:Q.242, K:V.258 Salt bridges: K:R.65, K:R.65

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain K: C.141, C.144, C.166, C.177 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.141, K:C.144, K:C.166, K:C.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z.A. et al., Structural Basis of Sirtuin 6-Catalyzed Nucleosome Deacetylation. J.Am.Chem.Soc. (2023)

Release Date

2023-04-05

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B: DH
NAD-dependent protein deacylase sirtuin-6: 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

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B

NAD-dependent protein deacylase sirtuin-6

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