SAXSdb — 8sdx

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

ATPase family AAA domain-containing protein 2B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	histone H4S1CK5ac × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	histone H4S1CK5ac × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATD2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–136； UniProt 953–1085 Author chain B； PDBConstruct 4–136； UniProt 953–1085

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	8sdx
Deposition date deposition_date	2023-04-07
Structure title title	ATAD2B bromodomain in complex with histone H4 acetylated at lysine 5 with Serine 1 mutation to Cysteine
Keywords keywords	bromodomains, Epigenetics, chromatin reader domain, protein binding, NUCLEAR PROTEIN; NUCLEAR 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.

8sdx__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8sdx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8sdx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.11 Å
Rg (electron density)	17.23 Å
Total Rg	18.12 Å
Atom count	1155
Residues	141
Excluded volume	20593 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8sdx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8sdx__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	ATPase family AAA domain-containing protein 2B
Molecular weight formula_weight	15826.1 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	2342

GPLEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIKR

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 polymer

Description description	histone H4S1CK5ac
Molecular weight formula_weight	1347.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

CGRGKGGKGLGKGGA

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

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Unit-cell length a length_a	47.687 Å
Unit-cell length b length_b	79.629 Å
Unit-cell length c length_c	64.348 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.14 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.690 Å
Low-resolution limit resolution_low	33.520 Å
R factor r_factor	0.2262
R_work r_work	0.2242
R_free r_free	0.2604

ATAD2B bromodomain in complex with histone H4 acetylated at lysine 5 with Serine 1 mutation to Cysteine

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

ATPase family AAA domain-containing protein 2B

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

8sdx__assembly_2__model_1

8sdx__assembly_2__model_1 | I(q)

8sdx__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

ATAD2B bromodomain in complex with histone H4 acetylated at lysine 5 with Serine 1 mutation to Cysteine

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

ATPase family AAA domain-containing protein 2B

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

8sdx__assembly_2__model_1

8sdx__assembly_2__model_1 | I(q)

8sdx__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)