› 8oiz

X-ray diffraction
2.5Å resolution

Crystal structure of human CRBN-DDB1 in complex with Pomalidomide

Released:
DOI: 10.2210/pdb8oiz/pdb
Model geometry
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PDB entry 8oiz coloured by chain, front view.
PDB entry 8oiz coloured by chain, side view.
PDB entry 8oiz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A degron blocking strategy towards improved CRL4CRBN recruiting PROTAC selectivity.
Bouguenina H, Scarpino A, O'Hanlon J, Warne J, Wang HZ, Chan Wah Hak L, Sadok A, McAndrew PC, Stubbs M, Pierrat OA, Hahner T, Cabry MP, Le Bihan YV, Mitsopoulos C, Sialana FJ, Roumeliotis TI, Burke R, Van Montfort RLM, Choudhary J, Chopra R, Caldwell JJ, Collins I
Chembiochem e202300351 (2023)
PMID: 37418539

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172480 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
DNA damage-binding protein 1 Chain: A
Molecule details ›
Chain: A
Length: 1148 amino acids
Theoretical weight: 128.14 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
Protein cereblon Chain: B
Molecule details ›
Chain: B
Length: 407 amino acids
Theoretical weight: 46.74 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q96SW2 (Residues: 40-442; Coverage: 91%)
Gene names: AD-006, CRBN
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand EDO 6 x EDO
Ligand ZN 1 x ZN
Ligand Y70 1 x Y70
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 71.841Å b: 128.508Å c: 198.377Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.213 0.262
Expression system: Spodoptera frugiperda

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