6VYJ: Human UHRF1 TTD domain

Human UHRF1 TTD domain in complex with a fragment. Determined by X-ray diffraction at 1.39 Å resolution. Released 27 Jan 2021.

Method: X-ray diffraction
Resolution: 1.39 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,398
Mol. weight: 19.61 kDa
Ligands: BGC, RVV
Released: 27 Jan 2021

Explore 6VYJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VYJ contains 8 α-helices and 12 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	126-128	3	1
β-strand	140-144	5	1
β-strand	151-162	12	1
α-helix	163-165	3
β-strand	183-188	6	1
α-helix	192-194	3
β-strand	196-200	5	1
α-helix	201-203	3
β-strand	204-205	2	1
α-helix	206-208	3
β-strand	211	1	2
α-helix	214-216	3
β-strand	222-227	6	2
β-strand	237-248	12	2
β-strand	253-259	7	2
β-strand	266-270	5	2
α-helix	271	1
α-helix	277	1
β-strand	278	1	2
α-helix	279-281	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	A	protein	164	Homo sapiens	Q96T88 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VYJ_1 E3 ubiquitin-protein ligase UHRF1 (chains A)
SNADEDMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALE
EDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWY
DAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERP

Ligands and cofactors

ID	Name	Formula	Copies
BGC	beta-D-glucopyranose	C6 H12 O6	1
RVV	2,4-dimethylpyridine	C7 H9 N	2

Primary citation

Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery. Chang, L., Campbell, J., Raji, I.O. et al. Sci Rep (2021) 11:1121-1121. DOI 10.1038/s41598-020-80588-4 · PubMed

Other PDB entries of the same protein (UniProt Q96T88 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W92 1.3 Å, Human UHRF1 TTD domain
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
3ZVZ 1.45 Å, PHD finger of human UHRF1
7FB7 1.45 Å, Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine
8XV6 1.6 Å, Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)
6B9M 1.68 Å, Crystal structure of UHRF1 TTD domain in complex with the polybasic region
6IIW 1.7 Å, Crystal structure of human UHRF1 PHD finger in complex with PAF15
3BI7 1.7 Å, Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF1
5YYA 1.7 Å, Crystal structure of Tandem Tudor Domain of human UHRF1
6VCS 1.7 Å, SRA domain of UHRF1 in complex with DNA
3FL2 1.75 Å, Crystal structure of the ring domain of the E3 ubiquitin-protein ligase UHRF1
3SHB 1.8 Å, Crystal Structure of PHD Domain of UHRF1

Browse structure collections

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