5SZC: Human Dpf3 double-PHD domain

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14. Determined by X-ray diffraction at 1.19 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 1.19 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,196
Mol. weight: 15.26 kDa
Ligands: ZN
Released: 16 Aug 2017

Explore 5SZC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5SZC contains 5 α-helices and 9 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	262	1	1
β-strand	272	1	2
β-strand	277	1	2
β-strand	282-283	2	1
β-strand	290-291	2	1
α-helix	300-306	7
β-strand	319	1	3
α-helix	328-330	3
β-strand	331-333	3	3
β-strand	340-342	3	3
α-helix	353-354	2
α-helix	361-367	7

Chain H: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	3
α-helix	4-10	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Zinc finger protein DPF3	A	protein	115	Homo sapiens	Q92784 (AlphaFold model)
Histone H3 tail peptide	H	protein	18	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5SZC_1 Zinc finger protein DPF3 (chains A)
GTVIPNNYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQC
IECKSCILCGTSENDDQLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLK

Sequence of entity 2 (H), FASTA

>5SZC_2 Histone H3 tail peptide (chains H)
ARTKQTARKSTGGKAPRK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (MPD) are not listed.

Primary citation

Identification of H3K4me1-associated proteins at mammalian enhancers. Local, A., Huang, H., Albuquerque, C.P. et al. Nat Genet (2018) 50:73-82. DOI 10.1038/s41588-017-0015-6 · PubMed

Other PDB entries of the same protein (UniProt Q92784 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5I3L 1.85 Å, DPF3b in complex with H3K14ac peptide
9UTH 2.69 Å, DPF3b in complex with H3K14cr peptide
2KWJ Solution structures of the double PHD fingers of human transcriptional protein DPF3…
2KWK Solution structures of the double PHD fingers of human transcriptional protein DPF3b…
2KWN Solution structure of the double PHD (plant homeodomain) fingers of human…
2KWO Solution structure of the double PHD (plant homeodomain) fingers of human…

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