6h0f

X-ray diffraction
3.25Å resolution

Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
DNA damage-binding protein 1 Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 856 amino acids
Theoretical weight: 95.77 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni cypovirus 15
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 73%)
  • Best match: Q16531-2 (Residues: 59-451)
Gene names: DDB1, XAP1
Sequence domains: CPSF A subunit region
Protein cereblon Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 426 amino acids
Theoretical weight: 48.98 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96SW2 (Residues: 36-442; Coverage: 92%)
Gene names: AD-006, CRBN
Sequence domains:
DNA-binding protein Ikaros Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 38 amino acids
Theoretical weight: 4.19 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13422 (Residues: 141-174; Coverage: 7%)
Gene names: IK1, IKAROS, IKZF1, LYF1, ZNFN1A1
Sequence domains: Zinc finger, C2H2 type

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 161.45Å b: 177.86Å c: 242.47Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.212 0.234
Expression systems:
  • Trichoplusia ni cypovirus 15
  • Trichoplusia ni