SAXSdb — 6xyx

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

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 heterocomplex	Heteromer	Protein 4	Nuclear receptor corepressor 1 × 2 （O75376） SODIUM ION × 2 1,2-ETHANEDIOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCL6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–126； UniProt 6–129 Author chain B； PDBConstruct 3–126； UniProt 6–129

Nuclear receptor corepressor 1

Homo sapiens

UniProt O75376

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	B-cell lymphoma 6 protein × 2 （P41182） SODIUM ION × 2 1,2-ETHANEDIOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCOR1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–17； UniProt 1340–1356 Author chain D； PDBConstruct 1–17； UniProt 1340–1356

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	6xyx
Deposition date deposition_date	2020-01-31
Structure title title	Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD corepressor peptide
Keywords keywords	BCL6, NCoR1., 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.

6xyx__assembly_1__model_1

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

Download this curve (.dat)

6xyx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6xyx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.35 Å
Rg (electron density)	19.47 Å
Total Rg	20.51 Å
Atom count	2198
Residues	270
Excluded volume	39527 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6xyx__assembly_1__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	B-cell lymphoma 6 protein
Molecular weight formula_weight	14498.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2506

GPDSQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE

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

Entity 2 Entity 2 polymer

Description description	Nuclear receptor corepressor 1
Molecular weight formula_weight	1942.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C

GITTIKEMGRSIHEIPR

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

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6xyxa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d6xyxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

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Unit-cell length a length_a	34.660 Å
Unit-cell length b length_b	64.520 Å
Unit-cell length c length_c	137.750 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	8

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

Resolution resolution	1.440 Å
Low-resolution limit resolution_low	21.630 Å
R factor r_factor	0.1686
R_work r_work	0.1670
R_free r_free	0.1978

Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD corepressor peptide

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

B-cell lymphoma 6 protein

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear receptor corepressor 1

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

6xyx__assembly_1__model_1

6xyx__assembly_1__model_1 | I(q)

6xyx__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD corepressor peptide

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

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

Nuclear receptor corepressor 1

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

6xyx__assembly_1__model_1

6xyx__assembly_1__model_1 | I(q)

6xyx__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)