5I3L: DPF3b

DPF3b in complex with H3K14ac peptide. Determined by X-ray diffraction at 1.85 Å resolution. Released 24 Feb 2016.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 2,010
Mol. weight: 28.6 kDa
Ligands: ZN
Released: 24 Feb 2016

Explore 5I3L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I3L contains 9 α-helices and 13 β-strands across 3 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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	257-259	3
β-strand	272	1	1
β-strand	277	1	1
β-strand	282-283	2	2
β-strand	290-291	2	2
α-helix	300-306	7
β-strand	319	1	3
β-strand	331-333	3	3
β-strand	340-342	3	3
α-helix	361-365	5

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	257-259	3
β-strand	262	1	4
β-strand	282-283	2	4
β-strand	290-291	2	4
α-helix	300-306	7
α-helix	328-330	3
β-strand	331-333	3	5
β-strand	340-342	3	5
α-helix	361-367	7

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	3
α-helix	4-11	8
α-helix	13-16	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Zinc finger protein DPF3	A, B	protein	115	Homo sapiens	Q92784 (AlphaFold model)
H3K14ac peptide	C	protein	21	synthetic construct	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5I3L_1 Zinc finger protein DPF3 (chains A, B)
GTVIPNNYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQC
IECKSCILCGTSENDDQLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLK

Sequence of entity 2 (C), FASTA

>5I3L_2 H3K14ac peptide (chains C)
ARTKQTARKSTGGKAPRKQLX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (NA, UNX, EDO) are not listed.

Primary citation

Crystal structure of DPF3b in complex with an acetylated histone peptide. Li, W., Zhao, A., Tempel, W. et al. J Struct Biol (2016) 195:365-372. DOI 10.1016/j.jsb.2016.07.001 · PubMed

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

5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
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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