7M10: PHF2 PHD Domain

PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1. Determined by X-ray diffraction at 1.15 Å resolution. Released 26 May 2021.

Method: X-ray diffraction
Resolution: 1.15 Å
Organism: Homo sapiens
Chains: 2
Atoms: 790
Mol. weight: 10.26 kDa
Ligands: ZN
Released: 26 May 2021

Explore 7M10 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M10 contains 4 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	39-44	6
β-strand	45-47	3	3
α-helix	54-57	4
β-strand	61-62	2	3

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	2
α-helix	5-7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase PHF2	A	protein	74	Homo sapiens	O75151 (AlphaFold model)
Serine/threonine-protein kinase VRK1 N-terminus peptide	B	protein	12	Homo sapiens	Q99986 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7M10_1 Lysine-specific demethylase PHF2 (chains A)
GSINMATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKT
HGKSTLKKKRTWHK

Sequence of entity 2 (B), FASTA

>7M10_2 Serine/threonine-protein kinase VRK1 N-terminus peptide (chains B)
PRVKAAQAGRQS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Histone H3 N-terminal mimicry drives a novel network of methyl-effector interactions. Chen, J., Horton, J., Sagum, C. et al. Biochem J (2021) 478:1943-1958. DOI 10.1042/BCJ20210203 · PubMed

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

3KQI 1.78 Å, crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide
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

Browse structure collections

About this viewer

MolViewer shows 7M10 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.