7usi

BRD2-BD1 in complex with MDP5

Method: X-RAY DIFFRACTION

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

Bromodomain-containing protein 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one × 1 DI(HYDROXYETHYL)ETHER × 4 1,2-ETHANEDIOL × 5 DIMETHYL SULFOXIDE × 1 CHLORIDE ION × 1 SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one × 1 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 8 DIMETHYL SULFOXIDE × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one × 1 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 2 DIMETHYL SULFOXIDE × 3 CHLORIDE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one × 1 1,2-ETHANEDIOL × 1 DIMETHYL SULFOXIDE × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one × 1 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 8 DIMETHYL SULFOXIDE × 1 CHLORIDE ION × 1 SODIUM ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one × 1 1,2-ETHANEDIOL × 3 DIMETHYL SULFOXIDE × 1 CHLORIDE ION × 1 TRIETHYLENE GLYCOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–114； UniProt 73–183 Author chain B； PDBConstruct 4–114； UniProt 73–183 Author chain C； PDBConstruct 4–114； UniProt 73–183 Author chain D； PDBConstruct 4–114； UniProt 73–183 Author chain E； PDBConstruct 4–114； UniProt 73–183 Author chain F； PDBConstruct 4–114； UniProt 73–183

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	7usi
Deposition date deposition_date	2022-04-25
Structure title title	BRD2-BD1 in complex with MDP5
Keywords keywords	Inhibitor, acetyllysine binding pocket, TRANSCRIPTON-INHIBITOR complex; TRANSCRIPTON/INHIBITOR
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.

7usi__assembly_1__model_1

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

Download this curve (.dat)

7usi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7usi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.43 Å
Rg (electron density)	14.53 Å
Total Rg	15.74 Å
Atom count	1003
Residues	111
Excluded volume	18259 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7usi__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7usi__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7usi__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7usi__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`7usi__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`7usi__assembly_6__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	Bromodomain-containing protein 2
Molecular weight formula_weight	13504.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5980

GPMGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQE

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 non-polymer

Description description	(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one
Molecular weight formula_weight	365.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	7

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	27

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 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	74

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	7usiA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	7usiB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	7usiC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	7usiD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	7usiE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	7usiF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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Unit-cell length a length_a	63.810 Å
Unit-cell length b length_b	149.872 Å
Unit-cell length c length_c	63.819 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	35.560 Å
R factor r_factor	0.2035
R_work r_work	0.2010
R_free r_free	0.2500

BRD2-BD1 in complex with MDP5

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

Bromodomain-containing protein 2

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

7usi__assembly_1__model_1

7usi__assembly_1__model_1 | I(q)

7usi__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 non-polymer

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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

BRD2-BD1 in complex with MDP5

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

Bromodomain-containing protein 2

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

7usi__assembly_1__model_1

7usi__assembly_1__model_1 | I(q)

7usi__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 non-polymer

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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)