SAXSdb — 6r0q

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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 heterocomplex	Heteromer	Protein 3	ALA-ALA-ALA × 1 ALA-ALA-ALA-ALA × 1 ZINC ION × 1 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid × 1 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	ALA-ALA-ALA × 2 ZINC ION × 1 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid × 1 water × 3	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 1 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid × 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 1–124； UniProt 1–124 Author chain B； PDBConstruct 1–124； UniProt 1–124 Author chain C； PDBConstruct 1–124； UniProt 1–124 Author chain D； PDBConstruct 1–124； 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	6r0q
Deposition date deposition_date	2019-03-13
Structure title title	Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide
Keywords keywords	SIGNALING PROTEIN, proteolysis targeting chimera, PROTAC, protein degradation, hydrolysis product; 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.

6r0q__assembly_1__model_1

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

Download this curve (.dat)

6r0q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6r0q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.64 Å
Rg (electron density)	13.18 Å
Total Rg	14.49 Å
Atom count	907
Residues	114
Excluded volume	15774 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6r0q__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6r0q__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6r0q__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6r0q__assembly_4__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 (6)

Entity 1 Entity 1 polymer

Description description	Cereblon isoform 4
Molecular weight formula_weight	13766.5 kDa
Mutation mutation	A52H, M54Y, F56H, R68N, A72R, I87V, L89Q
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3985

MPLDAGGQNSTQMVLAPGASIFRCRQCGQTISRRDWLLPMGGDHEHVVFNPHGYIHRVWCFSLAQGLNLIGRPSGEFSWFKGYDWTVAQCGQCGSHLGWHYEGGSQPQTFFGLIKDRLAEGPAD

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	ALA-ALA-ALA
Molecular weight formula_weight	273.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,E,G

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 polymer

Description description	ALA-ALA-ALA-ALA
Molecular weight formula_weight	358.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

XXXX

Source Source

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

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid
Molecular weight formula_weight	276.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	421

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Unit-cell length a length_a	61.728 Å
Unit-cell length b length_b	59.163 Å
Unit-cell length c length_c	61.751 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	49.170 Å
R factor r_factor	0.1594
R_work r_work	0.1578
R_free r_free	0.1904

Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide

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

6r0q__assembly_1__model_1

6r0q__assembly_1__model_1 | I(q)

6r0q__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide

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

6r0q__assembly_1__model_1

6r0q__assembly_1__model_1 | I(q)

6r0q__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)