2KWO: Histone peptide

Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing N-terminal acetylation at Serine 1. Determined by solution NMR. Released 14 Jul 2010.

Method: Solution NMR
Organism: Homo sapiens
Chains: 2
Atoms: 1,027
Mol. weight: 15.05 kDa
Ligands: ZN
Released: 14 Jul 2010

Explore 2KWO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2KWO contains 2 α-helices and 5 β-strands across 1 chain. 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	262	1	1
β-strand	290	1	1
α-helix	300-308	9
β-strand	319	1	2
β-strand	333-334	2	2
β-strand	339-340	2	2
α-helix	361-370	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone peptide	B	protein	20		P62805 (AlphaFold model)
Zinc finger protein DPF3	A	protein	114	Homo sapiens	Q92784 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>2KWO_1 Histone peptide (chains B)
SGRGKGGKGLGKGGAKRHRK

Sequence of entity 2 (A), FASTA

>2KWO_2 Zinc finger protein DPF3 (chains A)
GSYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECKS
CILCGTSENDDQLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLKEKAS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Zeng, L., Zhang, Q., Li, S. et al. Nature (2010) 466:258-262. DOI 10.1038/nature09139 · PubMed

Other PDB entries of the same protein (UniProt P62805 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F9X 1.25 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
8PEF 1.28 Å, Crystal structure of SLF1 Ankyrin repeat domain in complex with H4 tail (K20me0)
5TEG 1.3 Å, Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and…
3UVW 1.37 Å, Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated…
8UK5 1.4 Å, Crystal structure of the bromodomain of human ATAD2B in complex with histone H4S1(ph)K5ac
1ZKK 1.45 Å, Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy
4YY6 1.45 Å, Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide
3F9Y 1.5 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
3QZT 1.5 Å, Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form II
4YYI 1.5 Å, Crystal structure of BRD9 Bromodomain bound to an acetylated peptide
4YYM 1.5 Å, Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysine peptide
5FFW 1.5 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H4K5acK8ac histone…

Browse structure collections

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