7FB7: Human UHRF1 TTD

Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine. Determined by X-ray diffraction at 1.45 Å resolution. Released 5 Jan 2022.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,182
Mol. weight: 37.55 kDa
Ligands: 8NF
Released: 5 Jan 2022

Explore 7FB7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7FB7 contains 15 α-helices and 26 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: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	126	1	1
β-strand	127-129	3	2
β-strand	140-144	5	2
β-strand	151-162	12	2
α-helix	176-177	2
α-helix	179-181	3
β-strand	182-188	7	2
α-helix	192-194	3
β-strand	197-200	4	2
α-helix	201-203	3
β-strand	204-206	3	2
α-helix	207-208	2
β-strand	211	1	2
α-helix	214-216	3
β-strand	222-227	6	2
β-strand	237-248	12	2
β-strand	253-261	9	2
β-strand	264-271	8	2
α-helix	277	1
β-strand	278	1	2
α-helix	279-280	2

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	129	1	3
β-strand	140-144	5	3
β-strand	151-162	12	3
β-strand	181-188	8	3
α-helix	192-194	3
β-strand	196-200	5	3
α-helix	201-203	3
β-strand	204-206	3	3
α-helix	207-208	2
β-strand	211	1	3
α-helix	214-216	3
β-strand	222-227	6	3
β-strand	237-245	9	3
β-strand	252	1	1
β-strand	256-259	4	3
β-strand	266-270	5	3
α-helix	271	1
α-helix	277	1
β-strand	278	1	3
α-helix	279-281	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	A, B	protein	155	Homo sapiens	Q96T88 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7FB7_1 E3 ubiquitin-protein ligase UHRF1 (chains A, B)
SDEDMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRPALEEDVIYHVKYDD
YPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETR
TARELYANVVLGDDSLNDCRIIFVDEVFKIERPGE

Ligands and cofactors

ID	Name	Formula	Copies
8NF	5-amino-2,4-dimethylpyridine	C7 H10 N2	2

Water and common crystallization additives (MPD, SO4, DMS) are not listed.

Primary citation

Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1. Kori, S., Shibahashi, Y., Ekimoto, T. et al. Bioorg Med Chem (2021) 52:116500-116500. DOI 10.1016/j.bmc.2021.116500 · 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
6VYJ 1.39 Å, Human UHRF1 TTD domain in complex with a fragment
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
3ZVZ 1.45 Å, PHD finger of human UHRF1
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

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