7BQV: Cereblon

Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide. Determined by X-ray diffraction at 1.8 Å resolution. Released 26 Aug 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,129
Mol. weight: 15.61 kDa
Ligands: ZN, F4U
Released: 26 Aug 2020

Explore 7BQV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BQV contains 3 α-helices and 12 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	320-323	4	1
β-strand	330-333	4	1
α-helix	334-336	3
β-strand	337	1	2
β-strand	346-350	5	2
β-strand	356-362	7	2
β-strand	368-375	8	2
β-strand	384-391	8	2
β-strand	397-404	8	2
β-strand	413-418	6	2
α-helix	419-421	3
β-strand	422-423	2	1

Chain B: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	410-411	2	3
β-strand	418-419	2	3
α-helix	422-430	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	A	protein	109	Homo sapiens	Q96SW2 (AlphaFold model)
Sal-like protein 4	B	protein	24	Homo sapiens	Q9UJQ4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7BQV_1 Protein cereblon (chains A)
CTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKASNLNLIGRPSTE
HSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTI

Sequence of entity 2 (B), FASTA

>7BQV_2 Sal-like protein 4 (chains B)
SFVCSVCGHRFTTKGNLKVHFHRH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
F4U	2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione	C13 H10 N2 O5	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide. Furihata, H., Yamanaka, S., Honda, T. et al. Nat Commun (2020) 11:4578-4578. DOI 10.1038/s41467-020-18488-4 · PubMed

Other PDB entries of the same protein (UniProt Q96SW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4M91 1.1 Å, crystal structure of hN33/Tusc3-peptide 1
9CUO 1.6 Å, Crystal structure of CRBN with compound 3
9OHQ 1.6 Å, Structure of CRBN:IKZF2:Compound 15
9DOM 1.69 Å, PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of…
9O91 1.86 Å, Structure of IKZF2:CRBN:Compound 5 ternary structure
7BQU 1.9 Å, Cereblon in complex with SALL4 and (S)-thalidomide
9GAO 1.95 Å, Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-me…
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
8RQC 2.15 Å, Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2
8RQ8 2.19 Å, Crystal structure of CRBN-midi in complex with mezigdomide
9OHR 2.34 Å, Structure of CRBN:IKZF2:Compound 35
9SFM 2.39 Å, Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide

Browse structure collections

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