SMTL ID : 6yn1.1 (3 other biounits)

Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

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

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: N.99, Q.101 Chain H: Q.19, E.69, N.72 Chain I: G.23, G.24 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain H Water bridges: A:N.99, A:N.99, A:N.99, A:Q.101 Hydrogen bonds: H:Q.19, H:N.72 GOL.2: 3 residues within 4Å: Chain C: R.27 Chain D: T.12, R.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.12, D:T.12, D:R.18, D:R.18 GOL.3: 8 residues within 4Å: Chain H: Y.63, R.92, E.97 Chain I: V.42, F.43, N.46, Q.75, R.77 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:Q.75, I:R.77, H:R.92, H:E.97

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

CL.4: 2 residues within 4Å: Chain J: Y.29, E.30 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Corbeski, I. et al., Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. Sci Adv (2022)

Release Date

2021-11-17

Peptides

Histone H2A: AF
Histone H2B: BG
Histone H3: CH
Histone H4: DI
Aprataxin and PNK-like factor: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
F

B
B

G
G

C
C

H
H

D
D

I
I

E
E

J
J

Histone H2A

Histone H2B

Histone H3

Histone H4

Aprataxin and PNK-like factor

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