SMTL ID : 6axj.1 (5 other biounits)

Crystal structure of the Yaf9 YEATS domain bound to H3K27ac

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-3-3-mer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: H.65, F.90, D.91, R.112 Chain B: K.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.65, A:D.91 Water bridges: A:D.91, A:D.91, A:D.91, A:R.112, A:R.112 Salt bridges: A:R.112 SO4.2: 2 residues within 4Å: Chain A: K.63, D.66 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.63 Salt bridges: A:K.63 SO4.5: 5 residues within 4Å: Chain C: H.65, F.90, D.91, R.112 Chain D: K.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.65, C:D.91 Water bridges: C:D.91, C:D.91, C:D.91, C:R.112, C:R.112 Salt bridges: C:R.112 SO4.6: 2 residues within 4Å: Chain C: K.63, D.66 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.63 Salt bridges: C:K.63 SO4.9: 5 residues within 4Å: Chain E: H.65, F.90, D.91, R.112 Chain F: K.7 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:H.65, E:D.91 Water bridges: E:D.91, E:D.91, E:D.91, E:R.112, E:R.112 Salt bridges: E:R.112 SO4.10: 2 residues within 4Å: Chain E: K.63, D.66 2 PLIP interactions: 2 interactions with chain E Water bridges: E:K.63 Salt bridges: E:K.63

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.18, Y.147, D.149 Chain E: E.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.18, A:Y.18 GOL.4: 4 residues within 4Å: Chain A: T.21, F.44, R.46, E.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.21, A:T.21, A:R.46 Water bridges: A:E.81 GOL.7: 4 residues within 4Å: Chain A: E.155 Chain C: Y.18, Y.147, D.149 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.18, C:Y.18 GOL.8: 4 residues within 4Å: Chain C: T.21, F.44, R.46, E.81 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.21, C:T.21, C:R.46 Water bridges: C:E.81 GOL.11: 4 residues within 4Å: Chain C: E.155 Chain E: Y.18, Y.147, D.149 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.18, E:Y.18 GOL.12: 4 residues within 4Å: Chain E: T.21, F.44, R.46, E.81 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.21, E:T.21, E:R.46 Water bridges: E:E.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klein, B.J. et al., Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain. Nucleic Acids Res. (2018)

Release Date

2017-11-22

Peptides

Protein AF-9 homolog: ACE
ALY-SER-ALA-PRO-ALA: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
E

D
E

F
E

Protein AF-9 homolog

ALY-SER-ALA-PRO-ALA

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