3PTR: PHF2 Jumonji domain

PHF2 Jumonji domain. Determined by X-ray diffraction at 1.95 Å resolution. Released 26 Jan 2011.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,230
Mol. weight: 45.89 kDa
Released: 26 Jan 2011

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

Secondary structure: helices and β-sheets

3PTR contains 22 α-helices and 16 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 B: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	81-83	3
α-helix	87-95	9
β-strand	100	1	1
α-helix	101-103	3
β-strand	106-107	2	2
α-helix	110-112	3
α-helix	115-121	7
β-strand	127-129	3	2
β-strand	138	1	3
α-helix	146-153	8
β-strand	158-163	6	2
β-strand	168-173	6	2
α-helix	174-182	9
β-strand	190-196	7	2
α-helix	201-205	5
β-strand	207	1	3
α-helix	210-215	6
α-helix	217-221	5
α-helix	229-231	3
β-strand	236-240	5	2
β-strand	244-249	6	1
α-helix	252-254	3
β-strand	256-263	8	2
β-strand	266-271	6	1
α-helix	275-286	12
α-helix	290-292	3
α-helix	295-298	4
β-strand	303-307	5	1
β-strand	312-315	4	2
β-strand	320-325	6	1
β-strand	329-336	8	2
α-helix	342-355	14
α-helix	366-387	22
α-helix	389-392	4
α-helix	393-410	18
α-helix	419-421	3
α-helix	422-423	2
α-helix	428-443	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PHD finger protein 2	B	protein	392	Homo sapiens	O75151 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>3PTR_1 PHD finger protein 2 (chains B)
STLKKKRTWHKHGPGQAPDVKPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYME
EHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVD
YYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLI
CVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQV
DKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGS
LTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHE
DELPEHFKPSQLIKDLAKEIRLSENASKAVRP

Primary citation

Structural basis for human PHF2 Jumonji domain interaction with metal ions. Horton, J.R., Upadhyay, A.K., Hashimoto, H. et al. J Mol Biol (2011) 406:1-8. DOI 10.1016/j.jmb.2010.12.013 · 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
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
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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