SMTL ID : 5szb.2 (1 other biounit)

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with acetylated K14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

hetero-2-2-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.9, F.11, C.12, N.19, H.39, C.42 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.9, A:C.12, A:H.39, A:C.42 ZN.2: 6 residues within 4Å: Chain A: C.31, D.33, C.34, R.36, C.60, C.63 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.31, A:C.34, A:C.60, A:C.63 ZN.3: 6 residues within 4Å: Chain A: C.66, L.68, C.69, H.89, Y.91, C.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:H.89, A:C.92 ZN.4: 6 residues within 4Å: Chain A: C.81, D.83, C.84, R.86, C.107, C.110 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.81, A:C.84, A:C.107, A:C.110 ZN.6: 6 residues within 4Å: Chain C: C.9, F.11, C.12, N.19, H.39, C.42 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.9, C:C.12, C:H.39, C:C.42 ZN.7: 6 residues within 4Å: Chain C: C.31, D.33, C.34, R.36, C.60, C.63 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.31, C:C.34, C:C.60, C:C.63 ZN.8: 6 residues within 4Å: Chain C: C.66, L.68, C.69, H.89, Y.91, C.92 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.66, C:C.69, C:H.89, C:C.92 ZN.9: 6 residues within 4Å: Chain C: C.81, D.83, C.84, R.86, C.107, C.110 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.81, C:C.84, C:C.107, C:C.110

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 5 residues within 4Å: Chain A: R.24, P.25 Chain C: W.111, E.112, K.115 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.111, C:W.111 MPD.10: 5 residues within 4Å: Chain A: W.111, E.112, K.115 Chain C: R.24, P.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.111, A:W.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Local, A. et al., Identification of H3K4me1-associated proteins at mammalian enhancers. Nat. Genet. (2018)

Release Date

2017-08-16

Peptides

Zinc finger protein DPF3: AC
Histone H3 tail peptide: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
H

D
H

Zinc finger protein DPF3

Histone H3 tail peptide

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