5TDR: Set3 PHD finger

Set3 PHD finger in complex with histone H3K4me2. Determined by X-ray diffraction at 1.42 Å resolution. Released 2 Nov 2016.

Method: X-ray diffraction
Resolution: 1.42 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 2
Atoms: 867
Mol. weight: 9.5 kDa
Ligands: ZN
Released: 2 Nov 2016

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

Secondary structure: helices and β-sheets

5TDR contains 3 α-helices and 4 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, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	15-18	4	1
β-strand	25-27	3	1
α-helix	28-31	4
α-helix	36-38	3
α-helix	55-68	14

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-5	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SET domain-containing protein 3	A	protein	70	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P36124 (AlphaFold model)
Histone H3	B	protein	11	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5TDR_1 SET domain-containing protein 3 (chains A)
MGIITCICDLNDDDGFTIQCDHCNRWQHAICYGIKDIGMAPDDYLCNSCDPREVDINLAR
KIQQERINVK

Sequence of entity 2 (B), FASTA

>5TDR_2 Histone H3 (chains B)
ARTKQTARKST

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Structural Insight into Recognition of Methylated Histone H3K4 by Set3. Gatchalian, J., Ali, M., Andrews, F.H. et al. J Mol Biol (2017) 429:2066-2074. DOI 10.1016/j.jmb.2016.09.020 · PubMed

Other PDB entries of the same protein (UniProt P36124 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5TDW 1.7 Å, Set3 PHD finger in complex with histone H3K4me3

Browse structure collections

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