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

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).

Ligands and binding sites

• EF2 · S-Thalidomide · ligand · chains A
• JOE · 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-6-nitro-benzoic acid · ligand · chains B
• JOH · 2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione · ligand · chains C
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• PO4 · Phosphate ion · ion · 2 copies · chains A, B
• CL · Chloride ion · ion · chains A, B

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 625 Ų buried · 9 hydrogen bonds · protein-protein
• A–C · 612 Ų buried · 6 hydrogen bonds · protein-protein
• B–F · 91 Ų buried · 2 hydrogen bonds · protein-protein
• A–F · 38 Ų buried · 0 hydrogen bonds · protein-protein
• B–C · 21 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6R0S · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a 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 6R0S · PDBe 6R0S · UniProt A4TVL0