› 7ps9

X-ray diffraction
1.8Å resolution

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide (CC-220)

Released:
DOI: 10.2210/pdb7ps9/pdb
PDB entry 7ps9 coloured by chain, front view.
PDB entry 7ps9 coloured by chain, side view.
PDB entry 7ps9 coloured by chain, top view.
Source organism: Magnetospirillum gryphiswaldense
Primary publication:
High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system.
Heim C, Hartmann MD
Acta Crystallogr D Struct Biol 78 290-298 (2022)
PMID: 35234143

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107419 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
CULT domain-containing protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 124 amino acids
Theoretical weight: 13.63 KDa
Source organism: Magnetospirillum gryphiswaldense
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A4TVL0 (Residues: 1-124; Coverage: 100%)
Gene name: MGR_0879

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand 8W7 3 x 8W7
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 56.001Å b: 58.85Å c: 88.583Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.193 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 citation in other articles

Molecular glue CELMoD compounds are regulators of cereblon conformation.
Watson et al. (2022)
3 more

1 mention without citation

High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system.
Heim et al. (2022)