SAXSdb — 7lek

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

Bromodomain testis-specific protein

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	;11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one ; × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one ; × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one ; × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	;11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRDT_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–117； UniProt 266–378 Author chain B； PDBConstruct 5–117； UniProt 266–378 Author chain C； PDBConstruct 5–117； UniProt 266–378 Author chain D； PDBConstruct 5–117； UniProt 266–378

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	7lek
Deposition date deposition_date	2021-01-14
Structure title title	Crystal structure of the second bromodomain (BD2) of human BRDT bound to ERK5-IN-1
Keywords keywords	BRDT, BET, PLK1, testis specific, Bromodomain, GENE REGULATION; GENE REGULATION
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.

7lek__assembly_2__model_1

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

Download this curve (.dat)

7lek__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7lek__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.01 Å
Rg (electron density)	15.05 Å
Total Rg	16.20 Å
Atom count	1004
Residues	116
Excluded volume	18028 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7lek__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7lek__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7lek__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7lek__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 (5)

Entity 1 Entity 1 polymer

Description description	Bromodomain testis-specific protein
Molecular weight formula_weight	13704.8 kDa
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	3997

GAASTVKVTEQLRHCSEILKEMLAKKHFSYAWPFYNPVDVNALGLHNYYDVVKNPMDLGTIKEKMDNQEYKDAYKFAADVRLMFMNCYKYNPPDHEVVTMARMLQDVFETHFSKIPI

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	;11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one ;
Molecular weight formula_weight	638.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	nat
Copy count entity_count	1

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	56

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d7leka_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

Domain ID domain_id	d7lekb1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

Domain ID domain_id	d7lekb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d7lekc_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

Domain ID domain_id	d7lekd1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

Domain ID domain_id	d7lekd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	110.610 Å
Unit-cell length b length_b	99.320 Å
Unit-cell length c length_c	60.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	52.480 Å
R factor r_factor	0.2159
R_work r_work	0.2133
R_free r_free	0.2643

Crystal structure of the second bromodomain (BD2) of human BRDT bound to ERK5-IN-1

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

Bromodomain testis-specific 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

7lek__assembly_2__model_1

7lek__assembly_2__model_1 | I(q)

7lek__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

7. Citations (1)

Crystal structure of the second bromodomain (BD2) of human BRDT bound to ERK5-IN-1

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

Bromodomain testis-specific 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

7lek__assembly_2__model_1

7lek__assembly_2__model_1 | I(q)

7lek__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

7. Citations (1)