3KQI: PHF2 PHD domain

crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide. Determined by X-ray diffraction at 1.78 Å resolution. Released 2 Feb 2010.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Homo sapiens
Chains: 2
Atoms: 758
Mol. weight: 10.23 kDa
Ligands: ZN, MG
Released: 2 Feb 2010

Explore 3KQI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KQI contains 3 α-helices and 7 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: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	1
β-strand	12-13	2	1
β-strand	20-22	3	2
β-strand	29-31	3	2
α-helix	32-35	4
α-helix	42-44	3
β-strand	45	1	3
α-helix	51-57	7
β-strand	62	1	3

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PHD finger protein 2	A	protein	75	Homo sapiens	O75151 (AlphaFold model)
H3K4Me3 peptide	B	protein	12		P68431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3KQI_1 PHD finger protein 2 (chains A)
GPLGSMATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEK
THGKSTLKKKRTWHK

Sequence of entity 2 (B), FASTA

>3KQI_2 H3K4Me3 peptide (chains B)
ARTKQTARKSTG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	2

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation. Wen, H., Li, J., Song, T. et al. J Biol Chem (2010) 285:9322-9326. DOI 10.1074/jbc.C109.097667 · PubMed

Other PDB entries of the same protein (UniProt O75151 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M10 1.15 Å, PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1
3PUA 1.89 Å, PHF2 Jumonji-NOG-Ni(II)
3PU8 1.94 Å, PHF2 Jumonji-NOG-Fe(II) complex
3PU3 1.95 Å, PHF2 Jumonji domain-NOG complex
3PTR 1.95 Å, PHF2 Jumonji domain
3PUS 2.08 Å, PHF2 Jumonji-NOG-Ni(II)
8F8Y 3.06 Å, PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide
8F8Z 3.3 Å, PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide

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