6r0s

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cereblon isoform 4

Magnetospirillum gryphiswaldense MSR-1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 S-Thalidomide × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CEREBLON ISOFORM 4 × 1 ZINC ION × 1 PHOSPHATE ION × 1 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-6-nitro-benzoic acid × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4TVL0_9PROT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–125； UniProt 1–124 Author chain B； PDBConstruct 2–125； UniProt 1–124 Author chain C； PDBConstruct 2–125； UniProt 1–124

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6r0s
Deposition date deposition_date	2019-03-13
Structure title title	Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product
Keywords keywords	----, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6r0s__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6r0s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6r0s__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	14.49 Å
Rg (electron density)	13.13 Å
Total Rg	14.45 Å
Atom count	877
Residues	109
Excluded volume	15382 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6r0s__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6r0s__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6r0s__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Cereblon isoform 4
Molecular weight formula_weight	13703.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2871

AMPLDAGGQNSTQMVLAPGASIFRCRQCGQTISRRDWLLPMGGDHEHVVFNPAGMIFRVWCFSLAQGLRLIGAPSGEFSWFKGYDWTIALCGQCGSHLGWHYEGGSQPQTFFGLIKDRLAEGPAD

Source Source

Source organism organism	Magnetospirillum gryphiswaldense MSR-1
NCBI taxonomy ID ncbi_taxonomy_id	431944
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CEREBLON ISOFORM 4
Molecular weight formula_weight	273.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

XXX

Source Source

Source organism organism	Magnetospirillum gryphiswaldense MSR-1
NCBI taxonomy ID ncbi_taxonomy_id	431944
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	S-Thalidomide
Molecular weight formula_weight	258.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-6-nitro-benzoic acid
Molecular weight formula_weight	307.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione
Molecular weight formula_weight	289.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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Unit-cell length a length_a	56.455 Å
Unit-cell length b length_b	58.824 Å
Unit-cell length c length_c	88.234 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	44.120 Å
R factor r_factor	0.1882
R_work r_work	0.1868
R_free r_free	0.2129

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cereblon isoform 4

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6r0s__assembly_1__model_1

6r0s__assembly_1__model_1 | I(q)

6r0s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cereblon isoform 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6r0s__assembly_1__model_1

6r0s__assembly_1__model_1 | I(q)

6r0s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)