› 6h0g

X-ray diffraction
4.25Å resolution

Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4)

Released:
DOI: 10.2210/pdb6h0g/pdb
PDB entry 6h0g coloured by chain, front view.
PDB entry 6h0g coloured by chain, side view.
PDB entry 6h0g coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN.
Sievers QL, Petzold G, Bunker RD, Renneville A, Słabicki M, Liddicoat BJ, Abdulrahman W, Mikkelsen T, Ebert BL, Thomä NH
Science 362 (2018)
PMID: 30385546

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-172481 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
DNA damage-binding protein 1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 856 amino acids
Theoretical weight: 95.77 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 73%)
Gene names: DDB1, XAP1
Sequence domains:
Protein cereblon Chains: B, E
Molecule details ›
Chains: B, E
Length: 426 amino acids
Theoretical weight: 48.98 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96SW2 (Residues: 41-442; Coverage: 91%)
Gene names: AD-006, CRBN
Sequence domains:
Zinc finger protein 692 Chains: C, F
Molecule details ›
Chains: C, F
Length: 31 amino acids
Theoretical weight: 3.52 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BU19 (Residues: 413-442; Coverage: 6%)
Gene names: AREBP, ZFP692, ZNF692
Sequence domains: Zinc finger, C2H2 type

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand Y70 2 x Y70
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 112.51Å b: 99.53Å c: 166.94Å
α: 90° β: 108.49° γ: 90°
R-values:
R R work R free
0.223 0.221 0.256
Expression system: Trichoplusia ni

Quick links

Citations

61 review citations

PROTAC targeted protein degraders: the past is prologue.
Békés et al. (2022)
60 more

2 mentions without citation

Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.
Rui et al. (2023)
1 more