Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 5A and hydrolysis product

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).

Ligands and binding sites

• EF2 · S-Thalidomide · ligand · chains A
• JO8 · 3-azanyl-2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]benzoic acid · ligand · chains B
• JO5 · 4-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione · ligand · chains C
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
• CL · Chloride ion · ion · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–B · 603 Ų buried · 7 hydrogen bonds · protein-protein
• A–C · 487 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 6R0U · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5a and… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt A4TVL0
• Elsewhere: RCSB PDB 6R0U · PDBe 6R0U · UniProt A4TVL0