› 6y5p

X-ray diffraction
1.74Å resolution

RING-DTC domain of Deltex1 bound to NAD

Released:
DOI: 10.2210/pdb6y5p/pdb
PDB entry 6y5p coloured by chain, front view.
PDB entry 6y5p coloured by chain, side view.
PDB entry 6y5p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases.
Chatrin C, Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sumpton D, Sibbet GJ, Smith BO, Huang DT
Sci Adv 6 (2020)
PMID: 32948590

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183258 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase DTX1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 235 amino acids
Theoretical weight: 26.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86Y01 (Residues: 388-620; Coverage: 38%)
Gene name: DTX1
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand NAD 2 x NAD
Ligand EDO 8 x EDO
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 66.85Å b: 85.254Å c: 130.949Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.214
Expression system: Escherichia coli

Quick links

Citations

16 review citations

An expanded lexicon for the ubiquitin code.
Dikic et al. (2023)
15 more

1 mention without citation

Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases.
Chatrin et al. (2020)