› 6ccr

X-ray diffraction
1.6Å resolution

Selenomethionyl derivative of a GID4 fragment

Released:
DOI: 10.2210/pdb6ccr/pdb
PDB entry 6ccr coloured by chain, front view.
PDB entry 6ccr coloured by chain, side view.
PDB entry 6ccr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of GID4-mediated recognition of degrons for the Pro/N-end rule pathway.
Dong C, Zhang H, Li L, Tempel W, Loppnau P, Min J
Nat Chem Biol 14 466-473 (2018)
PMID: 29632410

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184880 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glucose-induced degradation protein 4 homolog Chain: A
Molecule details ›
Chain: A
Length: 186 amino acids
Theoretical weight: 21.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IVV7 (Residues: 116-300; Coverage: 62%)
Gene names: C17orf39, GID4, VID24
Sequence domains: Vacuolar import and degradation protein

Ligands and Environments

1 bound ligand:
Ligand UNX 36 x UNX
1 modified residue:
Ligand MSE 1 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 33.167Å b: 39.986Å c: 129.007Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.159 0.187
Expression system: Escherichia coli

Quick links

Citations

7 review citations

E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones.
Ishida et al. (2021)
6 more

2 mentions without citation

Recognition of nonproline N-terminal residues by the Pro/N-degron pathway.
Dong et al. (2020)
1 more