SAXSdb — 7rv4

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

Isoform 2 of B-cell lymphoma 6 protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;N-(3-chloropyridin-4-yl)-2-{5-(3-cyanophenyl)-3-[3-(1-methyl-1H-pyrazol-4-yl)prop-2-yn-1-yl]-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl}acetamide ; × 2 DIMETHYL SULFOXIDE × 2 SULFATE ION × 4 CHLORIDE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCL6_HUMAN
Isoform	P41182-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–127； UniProt 5–129

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	7rv4
Deposition date deposition_date	2021-08-18
Structure title title	Crystal structure of the BCL6 BTB domain in complex with OICR-9153
Keywords keywords	immunity, inflammatory response, transcription repressor, TRANSCRIPTION; TRANSCRIPTION
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.

7rv4__assembly_1__model_1

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

Download this curve (.dat)

7rv4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7rv4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.29 Å
Rg (electron density)	19.54 Å
Total Rg	20.57 Å
Atom count	4082
Residues	244
Excluded volume	36938 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7rv4__assembly_1__model_1`	dimeric （2）	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	Isoform 2 of B-cell lymphoma 6 protein
Molecular weight formula_weight	14559.8 kDa
Mutation mutation	C8Q,C67R,C84N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2277

GSADSQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	;N-(3-chloropyridin-4-yl)-2-{5-(3-cyanophenyl)-3-[3-(1-methyl-1H-pyrazol-4-yl)prop-2-yn-1-yl]-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl}acetamide ;
Molecular weight formula_weight	522.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	139

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Unit-cell length a length_a	30.702 Å
Unit-cell length b length_b	72.781 Å
Unit-cell length c length_c	55.514 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	30.050 Å
R factor r_factor	0.1204
R_work r_work	0.1189
R_free r_free	0.1474

Crystal structure of the BCL6 BTB domain in complex with OICR-9153

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

Isoform 2 of B-cell lymphoma 6 protein

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

7rv4__assembly_1__model_1

7rv4__assembly_1__model_1 | I(q)

7rv4__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of the BCL6 BTB domain in complex with OICR-9153

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

Isoform 2 of B-cell lymphoma 6 protein

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

7rv4__assembly_1__model_1

7rv4__assembly_1__model_1 | I(q)

7rv4__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)