5TDW: Set3 PHD finger

Set3 PHD finger in complex with histone H3K4me3. Determined by X-ray diffraction at 1.7 Å resolution. Released 19 Oct 2016.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 2
Atoms: 855
Mol. weight: 9.36 kDa
Ligands: ZN
Released: 19 Oct 2016

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

Secondary structure: helices and β-sheets

5TDW 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	69	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P36124 (AlphaFold model)
histone H3K4me3	B	protein	11	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5TDW_1 SET domain-containing protein 3 (chains A)
GIITCICDLNDDDGFTIQCDHCNRWQHAICYGIKDIGMAPDDYLCNSCDPREVDINLARK
IQQERINVK

Sequence of entity 2 (B), FASTA

>5TDW_2 histone H3K4me3 (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:

5TDR 1.42 Å, Set3 PHD finger in complex with histone H3K4me2

Browse structure collections

About this viewer

MolViewer shows 5TDW 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.