SMTL ID : 5vdc.1

Crystal structure of the human DPF2 tandem PHD finger domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.8, F.10, C.11, N.18, H.38, C.41 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.8, A:C.11, A:H.38, A:C.41 ZN.2: 6 residues within 4Å: Chain A: C.30, D.32, C.33, R.35, C.59, C.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.30, A:C.33, A:C.59, A:C.62 ZN.3: 6 residues within 4Å: Chain A: C.80, D.82, C.83, R.85, C.106, C.109 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.80, A:C.83, A:C.106, A:C.109 ZN.4: 6 residues within 4Å: Chain A: C.65, I.67, C.68, H.88, Y.90, C.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.65, A:C.68, A:H.88, A:C.91

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: F.10, R.35, L.42, F.44, W.57, C.59, I.60, K.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.60 Water bridges: A:R.35, A:W.57, A:E.61 GOL.6: 4 residues within 4Å: Chain A: L.92, T.93, P.94, S.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.95, A:S.95

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: I.67, Y.87, L.92, T.93, H.107, L.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.93 Water bridges: A:H.107, A:H.107 EDO.8: 8 residues within 4Å: Chain A: Y.55, R.56, Q.58, C.64, C.65, N.66, G.69, R.85 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.56, A:N.66, A:G.69 EDO.9: 3 residues within 4Å: Chain A: I.119, Y.120, Q.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, F.M. et al., Histone-binding of DPF2 mediates its repressive role in myeloid differentiation. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-05-24

Peptides

Zinc finger protein ubi-d4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Zinc finger protein ubi-d4