6L1F: PHF20L1 Tudor1

Crystal structure of PHF20L1 Tudor1 in complex with K142me1 DNMT1. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Sept 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 667
Mol. weight: 9.36 kDa
Released: 23 Sept 2020

Explore 6L1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L1F contains 2 α-helices and 7 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 B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8	1	1
β-strand	11	1	1
β-strand	18-22	5	2
β-strand	28-37	10	2
β-strand	42-47	6	2
α-helix	52-54	3
β-strand	56-59	4	2
β-strand	65-66	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
the K142me1 DNMT1 peptide	A	protein	6	Homo sapiens	P26358 (AlphaFold model)
PHD finger protein 20-like protein 1	B	protein	70	Homo sapiens	A8MW92 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6L1F_1 the K142me1 DNMT1 peptide (chains A)
RSKSDG

Sequence of entity 2 (B), FASTA

>6L1F_2 PHD finger protein 20-like protein 1 (chains B)
GSHMPPNRPGITFEIGARLEALDYLQKWYPSRIEKIDYEEGKMLVHFERWSHRYDEWIYW
DSNRLRPLER

Primary citation

Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1. Lv, M., Gao, J., Li, M. et al. J Phys Chem Lett (2020) 11:7932-7938. DOI 10.1021/acs.jpclett.0c02039 · PubMed

Other PDB entries of the same protein (UniProt P26358 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6X9J 1.79 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052
7SFC 1.97 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A
5WVO 2.0 Å, Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated…
5YDR 2.0 Å, Structure of DNMT1 RFTS domain in complex with ubiquitin
7SFF 2.05 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B
7SFD 2.09 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A
6X9I 2.2 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA
7XIB 2.23 Å, Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and…
6K3A 2.3 Å, Crystal structure of human PCNA in complex with DNMT1 PIP box motif.
3EPZ 2.31 Å, Structure of the replication foci-targeting sequence of human DNA cytosine…
7SFG 2.43 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM
3SWR 2.49 Å, Structure of human DNMT1 (601-1600) in complex with Sinefungin

Browse structure collections

About this viewer

MolViewer shows 6L1F 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.