5B79: DPF2 double PHD finger

Crystal structure of DPF2 double PHD finger. Determined by X-ray diffraction at 2.6 Å resolution. Released 26 Oct 2016.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 928
Mol. weight: 14.08 kDa
Ligands: ZN
Released: 26 Oct 2016

Explore 5B79 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B79 contains 8 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: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	1
β-strand	42-43	2	1
α-helix	52-57	6
α-helix	66-68	3
β-strand	71	1	2
α-helix	80-82	3
β-strand	83-85	3	2
α-helix	86	1
β-strand	92-94	3	2
α-helix	101-102	2
α-helix	105-106	2
α-helix	113-119	7
α-helix	120-122	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Zinc finger protein ubi-d4	A	protein	123	Homo sapiens	Q92785 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5B79_1 Zinc finger protein ubi-d4 (chains A)
SNNYCDFCLGDSKINKKTGQPEELVSCSDCGRSGHPSCLQFTPVMMAAVKTYRWQCIECK
CCNICGTSENDDQLLFCDDCDRGYHMYCLTPSMSEPPEGSWSCHLCLDLLKEKASIYQNQ
NSS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2. Xiong, X., Panchenko, T., Yang, S. et al. Nat Chem Biol (2016) 12:1111-1118. DOI 10.1038/nchembio.2218 · PubMed

Other PDB entries of the same protein (UniProt Q92785 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VDC 1.6 Å, Crystal structure of the human DPF2 tandem PHD finger domain
3IUF 1.8 Å, Crystal structure of the C2H2-type zinc finger domain of human ubi-d4
6LTH 3.0 Å, Structure of human BAF Base module
9RL4 3.5 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6
6LTJ 3.7 Å, Structure of nucleosome-bound human BAF complex
9RN2 4.1 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2
9RMC 4.2 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1
9RN1 5.9 Å, Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47…
9A0K A structural model of the endogenoushuman SWI/SNF (BAF) complex bound to the nucleosome…

Browse structure collections

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