Current Protein Identity：A4TVL0
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4V2Y Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide Deposited 2014-10-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M MAGNESIUM CHLORIDE, 0.1 M SODIUM CITRATE PH 5, 15%(W/V) PEG 4000
|
Resolution 1.40 Å R-free 0.195 |
| 4V2Y Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide Deposited 2014-10-15 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M MAGNESIUM CHLORIDE, 0.1 M SODIUM CITRATE PH 5, 15%(W/V) PEG 4000
|
Resolution 1.40 Å R-free 0.195 |
| 4V2Y Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide Deposited 2014-10-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M MAGNESIUM CHLORIDE, 0.1 M SODIUM CITRATE PH 5, 15%(W/V) PEG 4000
|
Resolution 1.40 Å R-free 0.195 |
| 4V2Z Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pomalidomide Deposited 2014-10-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M SODIUM ACETATE PH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.45 Å R-free 0.203 |
| 4V2Z Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pomalidomide Deposited 2014-10-15 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M SODIUM ACETATE PH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.45 Å R-free 0.203 |
| 4V2Z Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pomalidomide Deposited 2014-10-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M SODIUM ACETATE PH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.45 Å R-free 0.203 |
| 4V30 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Lenalidomide Deposited 2014-10-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 LVY S-Lenalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
15 %(W/V) PEG 6000, 5 %(W/V) GLYCEROL
|
Resolution 1.85 Å R-free 0.239 |
| 4V30 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Lenalidomide Deposited 2014-10-15 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 LVY S-Lenalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
15 %(W/V) PEG 6000, 5 %(W/V) GLYCEROL
|
Resolution 1.85 Å R-free 0.239 |
| 4V30 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Lenalidomide Deposited 2014-10-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 LVY S-Lenalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
15 %(W/V) PEG 6000, 5 %(W/V) GLYCEROL
|
Resolution 1.85 Å R-free 0.239 |
| 4V31 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine Deposited 2014-10-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 DUR 2'-DEOXYURIDINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M CITRIC ACID PH 3.5, 25 %(W/V) PEG 3350
|
Resolution 1.80 Å R-free 0.219 |
| 4V31 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine Deposited 2014-10-15 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 DUR 2'-DEOXYURIDINE × 1 FLC CITRATE ANION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M CITRIC ACID PH 3.5, 25 %(W/V) PEG 3350
|
Resolution 1.80 Å R-free 0.219 |
| 4V31 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine Deposited 2014-10-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 DUR 2'-DEOXYURIDINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.1 M CITRIC ACID PH 3.5, 25 %(W/V) PEG 3350
|
Resolution 1.80 Å R-free 0.219 |
| 4V32 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Y101F mutant Deposited 2014-10-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Mutation：YES | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.2 M SODIUM CHLORIDE, 0.1 M PHOSPHATE-CITRATE PH 4.2, 20 %(W/V) PEG 8000
|
Resolution 1.90 Å R-free 0.240 |
| 4V32 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Y101F mutant Deposited 2014-10-15 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Mutation：YES | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.2 M SODIUM CHLORIDE, 0.1 M PHOSPHATE-CITRATE PH 4.2, 20 %(W/V) PEG 8000
|
Resolution 1.90 Å R-free 0.240 |
| 4V32 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Y101F mutant Deposited 2014-10-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Mutation：YES | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
0.2 M SODIUM CHLORIDE, 0.1 M PHOSPHATE-CITRATE PH 4.2, 20 %(W/V) PEG 8000
|
Resolution 1.90 Å R-free 0.240 |
| 5AMH Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal crystal form Deposited 2015-03-10 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 7 NI NICKEL (II) ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
100 MM SODIUM ACETATE PH 4.6, 2.2 M CALCIUM CHLORIDE
|
Resolution 1.20 Å R-free 0.157 |
| 5AMI Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash I structure Deposited 2015-03-10 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
100 MM SODIUM ACETATE PH 4.6, 20 %(W/V) PEG 6000
|
Resolution 1.75 Å R-free 0.209 |
| 5AMI Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash I structure Deposited 2015-03-10 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
100 MM SODIUM ACETATE PH 4.6, 20 %(W/V) PEG 6000
|
Resolution 1.75 Å R-free 0.209 |
| 5AMI Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash I structure Deposited 2015-03-10 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
100 MM SODIUM ACETATE PH 4.6, 20 %(W/V) PEG 6000
|
Resolution 1.75 Å R-free 0.209 |
| 5AMJ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash II structure Deposited 2015-03-10 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
100 MM TRI-SODIUM CITRATE PH 5.6, 1.0 M AMMONIUM PHOSPHATE
|
Resolution 1.75 Å R-free 0.191 |
| 5AMJ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash II structure Deposited 2015-03-10 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
100 MM TRI-SODIUM CITRATE PH 5.6, 1.0 M AMMONIUM PHOSPHATE
|
Resolution 1.75 Å R-free 0.191 |
| 5AMJ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash II structure Deposited 2015-03-10 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
100 MM TRI-SODIUM CITRATE PH 5.6, 1.0 M AMMONIUM PHOSPHATE
|
Resolution 1.75 Å R-free 0.191 |
| 5AMK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form Deposited 2015-03-10 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
64 MM SODIUM CITRATE PH 7.0, 100 MM HEPES PH 7.0, 10 %(W/V) PEG 5000 MME
|
Resolution 2.90 Å R-free 0.217 |
| 5AMK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form Deposited 2015-03-10 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
64 MM SODIUM CITRATE PH 7.0, 100 MM HEPES PH 7.0, 10 %(W/V) PEG 5000 MME
|
Resolution 2.90 Å R-free 0.217 |
| 5AMK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form Deposited 2015-03-10 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
64 MM SODIUM CITRATE PH 7.0, 100 MM HEPES PH 7.0, 10 %(W/V) PEG 5000 MME
|
Resolution 2.90 Å R-free 0.217 |
| 5AMK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form Deposited 2015-03-10 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain D
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
64 MM SODIUM CITRATE PH 7.0, 100 MM HEPES PH 7.0, 10 %(W/V) PEG 5000 MME
|
Resolution 2.90 Å R-free 0.217 |
| 5OH1 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Aminoglutethimide Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate PH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.70 Å R-free 0.210 |
| 5OH1 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Aminoglutethimide Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate PH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.70 Å R-free 0.210 |
| 5OH1 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Aminoglutethimide Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9UQ (3~{R})-3-(4-aminophenyl)-3-ethyl-piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate PH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.70 Å R-free 0.210 |
| 5OH2 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pyrrolidin-2-one (Butyrolactam) Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 BAQ pyrrolidin-2-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.90 Å R-free 0.225 |
| 5OH2 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pyrrolidin-2-one (Butyrolactam) Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 BAQ pyrrolidin-2-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.90 Å R-free 0.225 |
| 5OH2 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pyrrolidin-2-one (Butyrolactam) Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 BAQ pyrrolidin-2-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.90 Å R-free 0.225 |
| 5OH3 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Ethosuximide Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9V2 (3~{S})-3-ethyl-3-methyl-pyrrolidine-2,5-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 2.10 Å R-free 0.231 |
| 5OH3 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Ethosuximide Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9V2 (3~{S})-3-ethyl-3-methyl-pyrrolidine-2,5-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 2.10 Å R-free 0.231 |
| 5OH3 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Ethosuximide Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 2.10 Å R-free 0.231 |
| 5OH4 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidine-2,6-dione (Glutarimide) Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9UZ piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 2.30 Å R-free 0.250 |
| 5OH4 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidine-2,6-dione (Glutarimide) Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9UZ piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 2.30 Å R-free 0.250 |
| 5OH4 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidine-2,6-dione (Glutarimide) Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9UZ piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 2.30 Å R-free 0.250 |
| 5OH7 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Imidazolidine-2,4-dione (Hydantoin) Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 HYN imidazolidine-2,4-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.85 Å R-free 0.203 |
| 5OH7 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Imidazolidine-2,4-dione (Hydantoin) Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 HYN imidazolidine-2,4-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.85 Å R-free 0.203 |
| 5OH7 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Imidazolidine-2,4-dione (Hydantoin) Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.85 Å R-free 0.203 |
| 5OH8 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Rolipram Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 ROL ROLIPRAM × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.95 Å R-free 0.220 |
| 5OH8 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Rolipram Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 ROL ROLIPRAM × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.95 Å R-free 0.220 |
| 5OH8 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Rolipram Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.95 Å R-free 0.220 |
| 5OH9 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thiazolidine-2,4-dione Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 OD3 1,3-thiazolidine-2,4-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.65 Å R-free 0.210 |
| 5OH9 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thiazolidine-2,4-dione Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 OD3 1,3-thiazolidine-2,4-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.65 Å R-free 0.210 |
| 5OH9 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thiazolidine-2,4-dione Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 OD3 1,3-thiazolidine-2,4-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.65 Å R-free 0.210 |
| 5OHA Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with 2-Thiohydantoin Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9UW 2-sulfanylideneimidazol-4-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.55 Å R-free 0.197 |
| 5OHA Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with 2-Thiohydantoin Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9UW 2-sulfanylideneimidazol-4-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.55 Å R-free 0.197 |
| 5OHA Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with 2-Thiohydantoin Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9UW 2-sulfanylideneimidazol-4-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.55 Å R-free 0.197 |
| 5OHB Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidin-2-one (Valerolactam) Deposited 2017-07-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 V1L piperidin-2-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.70 Å R-free 0.212 |
| 5OHB Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidin-2-one (Valerolactam) Deposited 2017-07-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 V1L piperidin-2-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.70 Å R-free 0.212 |
| 5OHB Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidin-2-one (Valerolactam) Deposited 2017-07-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 V1L piperidin-2-one × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
|
Resolution 1.70 Å R-free 0.212 |
| 6R0Q Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide Deposited 2019-03-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–124（124 aa）
|
Mutation：A52H, M54Y, F56H, R68N, A72R, I87V, L89Q | ZN ZINC ION × 1 JNW 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20 % PEG 3350, 0.2 M Ammonium acetate
|
Resolution 1.50 Å R-free 0.190 |
| 6R0Q Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide Deposited 2019-03-13 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Mutation：A52H, M54Y, F56H, R68N, A72R, I87V, L89Q | ZN ZINC ION × 1 JNW 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20 % PEG 3350, 0.2 M Ammonium acetate
|
Resolution 1.50 Å R-free 0.190 |
| 6R0Q Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide Deposited 2019-03-13 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–124（124 aa）
|
Mutation：A52H, M54Y, F56H, R68N, A72R, I87V, L89Q | ZN ZINC ION × 1 JNW 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20 % PEG 3350, 0.2 M Ammonium acetate
|
Resolution 1.50 Å R-free 0.190 |
| 6R0Q Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide Deposited 2019-03-13 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain D
1–124（124 aa）
|
Mutation：A52H, M54Y, F56H, R68N, A72R, I87V, L89Q | ZN ZINC ION × 1 JNW 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20 % PEG 3350, 0.2 M Ammonium acetate
|
Resolution 1.50 Å R-free 0.190 |
| 6R0S Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product Deposited 2019-03-13 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.55 Å R-free 0.213 |
| 6R0S Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product Deposited 2019-03-13 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 JOE 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-6-nitro-benzoic acid × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.55 Å R-free 0.213 |
| 6R0S Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product Deposited 2019-03-13 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JOH 2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.55 Å R-free 0.213 |
| 6R0U Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5a and hydrolysis product Deposited 2019-03-13 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.70 Å R-free 0.227 |
| 6R0U Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5a and hydrolysis product Deposited 2019-03-13 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 JO8 3-azanyl-2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]benzoic acid × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.70 Å R-free 0.227 |
| 6R0U Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5a and hydrolysis product Deposited 2019-03-13 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 JO5 4-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.70 Å R-free 0.227 |
| 6R0V Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with hydrolysis product of compound 4b Deposited 2019-03-13 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JO2 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-4-nitro-benzoic acid × 1 PO4 PHOSPHATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.60 Å R-free 0.219 |
| 6R0V Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with hydrolysis product of compound 4b Deposited 2019-03-13 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JO2 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-4-nitro-benzoic acid × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.60 Å R-free 0.219 |
| 6R0V Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with hydrolysis product of compound 4b Deposited 2019-03-13 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JO2 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-4-nitro-benzoic acid × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.60 Å R-free 0.219 |
| 6R11 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5b Deposited 2019-03-13 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JOB 5-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium Phosphate
|
Resolution 1.75 Å R-free 0.227 |
| 6R11 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5b Deposited 2019-03-13 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JOB 5-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium Phosphate
|
Resolution 1.75 Å R-free 0.227 |
| 6R11 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5b Deposited 2019-03-13 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium Phosphate
|
Resolution 1.75 Å R-free 0.227 |
| 6R12 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7b Deposited 2019-03-13 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.74 Å R-free 0.234 |
| 6R12 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7b Deposited 2019-03-13 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 JOT ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2-phenyl-ethanamide × 1 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.74 Å R-free 0.234 |
| 6R12 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7b Deposited 2019-03-13 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.74 Å R-free 0.234 |
| 6R13 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7f Deposited 2019-03-13 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.65 Å R-free 0.224 |
| 6R13 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7f Deposited 2019-03-13 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 JOK ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-phenyl-propanamide × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.65 Å R-free 0.224 |
| 6R13 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7f Deposited 2019-03-13 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.65 Å R-free 0.224 |
| 6R18 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 11a Deposited 2019-03-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.35 Å R-free 0.197 |
| 6R18 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 11a Deposited 2019-03-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 JOQ [4-(aminomethyl)phenyl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.35 Å R-free 0.197 |
| 6R18 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 11a Deposited 2019-03-14 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.35 Å R-free 0.197 |
| 6R19 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a Deposited 2019-03-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.45 Å R-free 0.201 |
| 6R19 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a Deposited 2019-03-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 2 JON [(2~{S})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.45 Å R-free 0.201 |
| 6R19 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a Deposited 2019-03-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.45 Å R-free 0.201 |
| 6R1A Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20b Deposited 2019-03-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 m Ammonium phosphate
|
Resolution 1.54 Å R-free 0.208 |
| 6R1A Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20b Deposited 2019-03-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 m Ammonium phosphate
|
Resolution 1.54 Å R-free 0.208 |
| 6R1A Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20b Deposited 2019-03-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 JP8 [(2~{R})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 m Ammonium phosphate
|
Resolution 1.54 Å R-free 0.208 |
| 6R1C Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a Deposited 2019-03-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ASP ASPARTIC ACID × 1 ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.50 Å R-free 0.215 |
| 6R1C Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a Deposited 2019-03-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 2 JOW 4-[[4-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyloxymethyl]phenyl]methylamino]-4-oxidanylidene-butanoic acid × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.50 Å R-free 0.215 |
| 6R1C Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a Deposited 2019-03-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.50 Å R-free 0.215 |
| 6R1D Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7d, co-crystallized Deposited 2019-03-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JP5 (phenylmethyl) ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；15 % PEG 6K, 5 % Glycerol
|
Resolution 1.10 Å R-free 0.150 |
| 6R1D Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7d, co-crystallized Deposited 2019-03-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JP5 (phenylmethyl) ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；15 % PEG 6K, 5 % Glycerol
|
Resolution 1.10 Å R-free 0.150 |
| 6R1K Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7c Deposited 2019-03-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JPB ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.94 Å R-free 0.212 |
| 6R1K Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7c Deposited 2019-03-14 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JPB ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.94 Å R-free 0.212 |
| 6R1K Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7c Deposited 2019-03-14 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JPB ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.94 Å R-free 0.212 |
| 6R1W Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 16b Deposited 2019-03-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium Phosphate
|
Resolution 1.35 Å R-free 0.198 |
| 6R1W Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 16b Deposited 2019-03-15 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 2 JPW (4-azanylcyclohexyl)methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium Phosphate
|
Resolution 1.35 Å R-free 0.198 |
| 6R1W Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 16b Deposited 2019-03-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 JPW (4-azanylcyclohexyl)methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium Phosphate
|
Resolution 1.35 Å R-free 0.198 |
| 6R1X Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7a Deposited 2019-03-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JPQ ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-methyl-but-2-enamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.80 Å R-free 0.216 |
| 6R1X Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7a Deposited 2019-03-15 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 JPQ ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-methyl-but-2-enamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.80 Å R-free 0.216 |
| 6R1X Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7a Deposited 2019-03-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.4 M Ammonium phosphate
|
Resolution 1.80 Å R-free 0.216 |
| 7PJK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with a benzotriazole analog of thalidomide Deposited 2021-08-24 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 7SE (3S)-3-(benzotriazol-2-yl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M (NH4)2HPO4
|
Resolution 1.99 Å R-free 0.254 |
| 7PJK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with a benzotriazole analog of thalidomide Deposited 2021-08-24 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 7SE (3S)-3-(benzotriazol-2-yl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M (NH4)2HPO4
|
Resolution 1.99 Å R-free 0.254 |
| 7PJK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with a benzotriazole analog of thalidomide Deposited 2021-08-24 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M (NH4)2HPO4
|
Resolution 1.99 Å R-free 0.254 |
| 7PS9 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide (CC-220) Deposited 2021-09-22 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.5 M (NH4)H2PO4
|
Resolution 1.80 Å R-free 0.246 |
| 7PS9 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide (CC-220) Deposited 2021-09-22 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.5 M (NH4)H2PO4
|
Resolution 1.80 Å R-free 0.246 |
| 7PS9 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide (CC-220) Deposited 2021-09-22 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.5 M (NH4)H2PO4
|
Resolution 1.80 Å R-free 0.246 |
| 7PSO Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Avadomide (CC-122) Deposited 2021-09-23 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.5 M (NH4)H2PO4
|
Resolution 1.52 Å R-free 0.217 |
| 7PSO Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Avadomide (CC-122) Deposited 2021-09-23 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.5 M (NH4)H2PO4
|
Resolution 1.52 Å R-free 0.217 |
| 7PSO Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Avadomide (CC-122) Deposited 2021-09-23 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 835 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.5 M (NH4)H2PO4
|
Resolution 1.52 Å R-free 0.217 |
| 7SHH Bacterial cereblon homologue in complex with (R)-3-(4-methoxyphenyl)piperidine-2,6-dione Deposited 2021-10-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9FT (3R)-3-(4-methoxyphenyl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0. 1M sodium acetate and 16% PEG 6000
|
Resolution 1.90 Å R-free 0.216 |
| 7SHH Bacterial cereblon homologue in complex with (R)-3-(4-methoxyphenyl)piperidine-2,6-dione Deposited 2021-10-08 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9FT (3R)-3-(4-methoxyphenyl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0. 1M sodium acetate and 16% PEG 6000
|
Resolution 1.90 Å R-free 0.216 |
| 7SHH Bacterial cereblon homologue in complex with (R)-3-(4-methoxyphenyl)piperidine-2,6-dione Deposited 2021-10-08 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 9FT (3R)-3-(4-methoxyphenyl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0. 1M sodium acetate and 16% PEG 6000
|
Resolution 1.90 Å R-free 0.216 |
| 8AOP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 14r Deposited 2022-08-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 MW6 (3S)-3-[(3-aminophenyl)sulfanylmethyl]piperidine-2,6-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.4M Ammonium Phosphate
|
Resolution 1.94 Å R-free 0.227 |
| 8AOP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 14r Deposited 2022-08-08 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 MW6 (3S)-3-[(3-aminophenyl)sulfanylmethyl]piperidine-2,6-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.4M Ammonium Phosphate
|
Resolution 1.94 Å R-free 0.227 |
| 8AOP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 14r Deposited 2022-08-08 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.4M Ammonium Phosphate
|
Resolution 1.94 Å R-free 0.227 |
| 8AOQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a Deposited 2022-08-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 N8F (3~{S})-3-(phenylsulfonylmethyl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.4M Ammonium Phosphate
|
Resolution 2.09 Å R-free 0.233 |
| 8AOQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a Deposited 2022-08-08 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 N8F (3~{S})-3-(phenylsulfonylmethyl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.4M Ammonium Phosphate
|
Resolution 2.09 Å R-free 0.233 |
| 8AOQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a Deposited 2022-08-08 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.4M Ammonium Phosphate
|
Resolution 2.09 Å R-free 0.233 |
| 8BC6 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aspartimide degron peptide Deposited 2022-10-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.72 Å R-free 0.223 |
| 8BC6 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aspartimide degron peptide Deposited 2022-10-15 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.72 Å R-free 0.223 |
| 8BC6 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aspartimide degron peptide Deposited 2022-10-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.72 Å R-free 0.223 |
| 8BC7 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aminoglutarimide degron peptide Deposited 2022-10-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.72 Å R-free 0.211 |
| 8BC7 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aminoglutarimide degron peptide Deposited 2022-10-15 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.72 Å R-free 0.211 |
| 8BC7 Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aminoglutarimide degron peptide Deposited 2022-10-15 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 EF2 S-Thalidomide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.72 Å R-free 0.211 |
| 8C3H Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex a long aspartimide degron peptide Deposited 2022-12-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；274 K；0.5 M (NH4)H2PO4
|
Resolution 1.71 Å R-free 0.210 |
| 8C3H Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex a long aspartimide degron peptide Deposited 2022-12-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；274 K；0.5 M (NH4)H2PO4
|
Resolution 1.71 Å R-free 0.210 |
| 8C3H Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex a long aspartimide degron peptide Deposited 2022-12-23 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；274 K；0.5 M (NH4)H2PO4
|
Resolution 1.71 Å R-free 0.210 |
| 8OU3 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 8d Deposited 2023-04-21 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–124（124 aa）
Chain B
1–124（124 aa）
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 3 EF2 S-Thalidomide × 2 PO4 PHOSPHATE ION × 3 W1T 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-fluoranyl-benzamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.47 Å R-free 0.238 |
| 8OU4 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11a Deposited 2023-04-21 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 W2F 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-chloranyl-benzamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 2.25 Å R-free 0.269 |
| 8OU4 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11a Deposited 2023-04-21 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 W2F 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-chloranyl-benzamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 2.25 Å R-free 0.269 |
| 8OU4 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11a Deposited 2023-04-21 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 2.25 Å R-free 0.269 |
| 8OU5 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11b Deposited 2023-04-21 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–124（124 aa）
Chain B
1–124（124 aa）
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 3 W1X 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-(trifluoromethyl)benzamide × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 2.30 Å R-free 0.253 |
| 8OU6 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11c Deposited 2023-04-21 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
20–123（104 aa）
Chain B
20–123（104 aa）
Chain C
20–123（104 aa）
|
Not recorded | ZN ZINC ION × 3 W26 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-methyl-benzamide × 2 PO4 PHOSPHATE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.84 Å R-free 0.225 |
| 8OU7 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11d Deposited 2023-04-22 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 W1F 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-methoxy-benzamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.70 Å R-free 0.224 |
| 8OU7 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11d Deposited 2023-04-22 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 W1F 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-methoxy-benzamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.70 Å R-free 0.224 |
| 8OU7 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11d Deposited 2023-04-22 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 W1F 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-methoxy-benzamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.70 Å R-free 0.224 |
| 8OU9 Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11e Deposited 2023-04-22 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
18–123（106 aa）
Chain B
18–123（106 aa）
Chain C
18–123（106 aa）
|
Not recorded | ZN ZINC ION × 3 W1B 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-oxidanyl-benzamide × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.75 Å R-free 0.224 |
| 8OUA Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11f Deposited 2023-04-22 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
19–123（105 aa）
Chain B
19–123（105 aa）
Chain C
18–123（106 aa）
|
Not recorded | ZN ZINC ION × 3 W0Z 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(fluoranyl)-3-methoxy-benzamide × 2 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；294 K；0.5 M (NH4)H2PO4
|
Resolution 1.85 Å R-free 0.238 |
| 8RDP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8a Deposited 2023-12-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ7 (5~{S})-3-(2-chlorophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.76 Å R-free 0.230 |
| 8RDP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8a Deposited 2023-12-08 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ7 (5~{S})-3-(2-chlorophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.76 Å R-free 0.230 |
| 8RDP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8a Deposited 2023-12-08 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ7 (5~{S})-3-(2-chlorophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.76 Å R-free 0.230 |
| 8RDQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8b Deposited 2023-12-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 YQO (5S)-3-(2,4-dichlorophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 2.03 Å R-free 0.249 |
| 8RDQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8b Deposited 2023-12-08 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 YQO (5S)-3-(2,4-dichlorophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 2.03 Å R-free 0.249 |
| 8RDQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8b Deposited 2023-12-08 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 2.03 Å R-free 0.249 |
| 8RDR Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8g Deposited 2023-12-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ3 (5~{S})-3-(2-nitrophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.58 Å R-free 0.214 |
| 8RDR Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8g Deposited 2023-12-08 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ3 (5~{S})-3-(2-nitrophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.58 Å R-free 0.214 |
| 8RDR Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8g Deposited 2023-12-08 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ3 (5~{S})-3-(2-nitrophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.58 Å R-free 0.214 |
| 8RDS Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8i Deposited 2023-12-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ6 (5~{S})-3-(2-methoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 2.00 Å R-free 0.253 |
| 8RDS Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8i Deposited 2023-12-08 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ6 (5~{S})-3-(2-methoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 2.00 Å R-free 0.253 |
| 8RDS Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8i Deposited 2023-12-08 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 2.00 Å R-free 0.253 |
| 8RDT Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8j Deposited 2023-12-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ2 (5~{S})-3-(2,3,4-trimethoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM Thalidomide
|
Resolution 1.95 Å R-free 0.242 |
| 8RDT Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8j Deposited 2023-12-08 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1HZ2 (5~{S})-3-(2,3,4-trimethoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM Thalidomide
|
Resolution 1.95 Å R-free 0.242 |
| 8RDT Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8j Deposited 2023-12-08 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM Thalidomide
|
Resolution 1.95 Å R-free 0.242 |
| 9GJQ Crystal structure of humanised cereblon from Magnetospirillum gryphiswaldense bound by dihydrouracil-indole compound [1-(1H-indol-6-yl)dihydro-2,4(1H,3H)-pyrimidinedione]. Deposited 2024-08-22 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
18–124（107 aa）
|
Mutation：A52H, M54Y, F56H, F77H, Y101F, R117A | A1IMN 1-(1H-indol-6-yl)-1,3-diazinane-2,4-dione × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10 % PEG8000, 8 % ethylene glycol and 100 mM Na-HEPES buffer (pH 7.5)
|
Resolution 1.39 Å R-free 0.209 |
| 9HTK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2n Deposited 2024-12-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IXA (3S)-3-phenylsulfanylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.49 Å R-free 0.210 |
| 9HTK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2n Deposited 2024-12-19 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1I4R (3R)-3-phenylsulfanylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.49 Å R-free 0.210 |
| 9HTK Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2n Deposited 2024-12-19 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IXA (3S)-3-phenylsulfanylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.49 Å R-free 0.210 |
| 9HTL Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2j Deposited 2024-12-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW9 (3~{R})-3-phenoxypiperidine-2,6-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.74 Å R-free 0.217 |
| 9HTL Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2j Deposited 2024-12-19 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW9 (3~{R})-3-phenoxypiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.74 Å R-free 0.217 |
| 9HTL Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2j Deposited 2024-12-19 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.74 Å R-free 0.217 |
| 9HTM Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2o Deposited 2024-12-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW8 (3R)-3-phenylazanylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.85 Å R-free 0.237 |
| 9HTM Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2o Deposited 2024-12-19 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW8 (3R)-3-phenylazanylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.85 Å R-free 0.237 |
| 9HTM Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2o Deposited 2024-12-19 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1I4P (3S)-3-phenylazanylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.85 Å R-free 0.237 |
| 9HTN Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2s Deposited 2024-12-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW7 (3R)-3-(3,4-dihydro-2H-quinolin-1-yl)piperidine-2,6-dione × 1 PO4 PHOSPHATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.92 Å R-free 0.235 |
| 9HTN Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2s Deposited 2024-12-19 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1I4Q (3S)-3-(3,4-dihydro-2H-quinolin-1-yl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.92 Å R-free 0.235 |
| 9HTN Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2s Deposited 2024-12-19 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1I4Q (3S)-3-(3,4-dihydro-2H-quinolin-1-yl)piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.92 Å R-free 0.235 |
| 9HTO Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2r Deposited 2024-12-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW6 (3~{S})-3-indol-1-ylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.85 Å R-free 0.240 |
| 9HTO Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2r Deposited 2024-12-19 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW6 (3~{S})-3-indol-1-ylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.85 Å R-free 0.240 |
| 9HTO Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2r Deposited 2024-12-19 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW6 (3~{S})-3-indol-1-ylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 1.85 Å R-free 0.240 |
| 9HTP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2p Deposited 2024-12-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 2.35 Å R-free 0.281 |
| 9HTP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2p Deposited 2024-12-19 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW5 (3~{S})-3-[methyl(phenyl)amino]piperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 2.35 Å R-free 0.281 |
| 9HTP Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2p Deposited 2024-12-19 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide
|
Resolution 2.35 Å R-free 0.281 |
| 9HTQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2u Deposited 2024-12-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW4 (3~{S})-3-carbazol-9-ylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.63 Å R-free 0.202 |
| 9HTQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2u Deposited 2024-12-19 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW4 (3~{S})-3-carbazol-9-ylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.63 Å R-free 0.202 |
| 9HTQ Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2u Deposited 2024-12-19 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–124（124 aa）
|
Not recorded | ZN ZINC ION × 1 A1IW4 (3~{S})-3-carbazol-9-ylpiperidine-2,6-dione × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
|
Resolution 1.63 Å R-free 0.202 |