7LKY: PHF1 Tudor domain

Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641. Determined by X-ray diffraction at 1.85 Å resolution. Released 15 Dec 2021.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, synthetic construct
Chains: 16
Atoms: 4,347
Mol. weight: 66.29 kDa
Ligands: ZN
Released: 15 Dec 2021

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

Secondary structure: helices and β-sheets

7LKY contains 8 α-helices and 45 β-strands across 13 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.

Chains A, C, D, F and G: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	1
β-strand	46-55	10	1
β-strand	60-65	6	1
β-strand	70-74	5	1
α-helix	75-77	3
β-strand	78-80	3	1

Chains B, E and H: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	2
β-strand	46-55	10	2
β-strand	60-64	5	2
β-strand	70-74	5	2
α-helix	75-77	3
β-strand	78-80	3	2

Chains J, K, L, O and P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 1 of PHD finger protein 1	A, B, C, D, E, F, G, H	protein	64	Homo sapiens	O43189 (AlphaFold model)
Peptidomimetic inhibitor UNC6641	I, J, K, L, M, N, O, P	protein	8	synthetic construct

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>7LKY_1 Isoform 1 of PHD finger protein 1 (chains A, B, C, D, E, F, G, H)
GPLGRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAAL
PGEE

Sequence of entity 2 (I, J, K, L, M, N, O, P), FASTA

>7LKY_2 Peptidomimetic inhibitor UNC6641 (chains I, J, K, L, M, N, O, P)
GGVXKPLR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

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

Primary citation

Discovery of an H3K36me3-Derived Peptidomimetic Ligand with Enhanced Affinity for Plant Homeodomain Finger Protein 1 (PHF1). Engelberg, I.A., Liu, J., Norris-Drouin, J.L. et al. J Med Chem (2021) 64:8510-8522. DOI 10.1021/acs.jmedchem.1c00430 · PubMed

Other PDB entries of the same protein (UniProt O43189 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WAV 1.7 Å, Crystal structure of PHF1 in complex with H3K36me3 substitution
6WAT 1.8 Å, complex structure of PHF1
4HCZ 1.85 Å, PHF1 Tudor in complex with H3K36me3
5XFN 1.9 Å, Structure of the N-terminal domains of PHF1
5XFO 1.9 Å, Structure of the N-terminal domains of PHF1
5XFP 2.3 Å, Binary complex of PHF1 and a double stranded DNA
8H43 2.3 Å, Crystal structure of PHF1 Tudor domain in complex with hit 1
2E5P Solution structure of the TUDOR domain of PHD finger protein 1 (PHF1 protein)
2M0O The solution structure of human PHF1 in complex with H3K36me3

Browse structure collections

About this viewer

MolViewer shows 7LKY 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.