SMTL ID : 5ye4.1 (1 other biounit)

Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

14 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.162 Chain B: D.166 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.166, B:D.166, A:H.162, H2O.12, H2O.13 ZN.2: 1 residues within 4Å: Chain A: E.16 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.16, H2O.6, H2O.7 ZN.3: 1 residues within 4Å: Chain A: E.89 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.89, A:E.89, H2O.2 ZN.4: 1 residues within 4Å: Chain A: D.31 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.31, A:D.31 ZN.5: 2 residues within 4Å: Chain A: E.10, K.19 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.10, A:E.10, H2O.2, H2O.5 ZN.6: 2 residues within 4Å: Chain A: D.62 Chain B: D.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.62, B:D.1, B:D.1 ZN.7: 2 residues within 4Å: Chain A: Q.39 Chain B: H.38 No protein-ligand interaction detected (PLIP) ZN.8: 1 residues within 4Å: Chain B: H.197 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.197, H2O.13, H2O.14 ZN.9: 3 residues within 4Å: Chain B: D.28, D.92 Chain C: R.3 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.92, B:D.92, H2O.11 ZN.10: 1 residues within 4Å: Chain B: D.1 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.1, H2O.8, H2O.10 ZN.11: 2 residues within 4Å: Chain B: D.70 Ligands: ZN.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.70, H2O.11 ZN.12: 2 residues within 4Å: Chain B: D.70 Ligands: ZN.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.70, B:D.70, H2O.10 ZN.13: 1 residues within 4Å: Chain B: D.142 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.142, B:D.142, H2O.14 ZN.14: 3 residues within 4Å: Chain B: E.184, R.187, H.188 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.184, B:E.184, B:H.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Handoko, L. et al., JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states. Epigenetics (2018)

Release Date

2018-08-22

Peptides

1A9D7 VH CH1 chain: A
1A9D7 L chain: B
di-acetylated histone H4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

1A9D7 VH CH1 chain

1A9D7 L chain

di-acetylated histone H4

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