SAXSdb — 4pkl

▼

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

Bromodomain factor 2

Trypanosoma brucei brucei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H,2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE × 1 PHOSPHATE ION × 1 POTASSIUM ION × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H,2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE × 1 POTASSIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q38AM1_TRYB2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–119； UniProt 9–123 Author chain B； PDBConstruct 5–119； UniProt 9–123

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4pkl
Deposition date deposition_date	2014-05-15
Structure title title	Bromodomain of Trypanosoma brucei BDF2 With IBET-151
Keywords keywords	SIGNALING PROTEIN, INHIBITOR, HISTONE, EPIGENETIC READER, SIGNALING PROTEIN-INHIBITOR complex; SIGNALING PROTEIN/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4pkl__assembly_2__model_1

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

Download this curve (.dat)

4pkl__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pkl__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	14.80 Å
Rg (electron density)	13.68 Å
Total Rg	14.83 Å
Atom count	902
Residues	108
Excluded volume	16000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pkl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4pkl__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Bromodomain factor 2
Molecular weight formula_weight	13500.1 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	2113

GPHMSFNKNGCLVFVSRLWDLDKLGMFHHPVSAEELPDYHTVIKRPVDLSSIRDGIEKGTYATDVDVQNDVARMITNALEYNAKGSTWYQEAMSFRKTYLDLARQSGLVVDDDEAYIPS

Source Source

Source organism organism	Trypanosoma brucei brucei
NCBI taxonomy ID ncbi_taxonomy_id	999953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H,2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE
Molecular weight formula_weight	415.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 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	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	274

▼

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4pkla1
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	d4pkla2
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	d4pklb_
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

CATH v4.4 (2 domains)

Domain ID domain_id	4pklA00
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	4pklB00
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

▶

Unit-cell length a length_a	55.869 Å
Unit-cell length b length_b	62.091 Å
Unit-cell length c length_c	62.117 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	1.251 Å
Low-resolution limit resolution_low	31.059 Å
R factor r_factor	0.1695
R_work r_work	0.1692
R_free r_free	0.1792

Bromodomain of Trypanosoma brucei BDF2 With IBET-151

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

Bromodomain factor 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

4pkl__assembly_2__model_1

4pkl__assembly_2__model_1 | I(q)

4pkl__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Bromodomain of Trypanosoma brucei BDF2 With IBET-151

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

Bromodomain factor 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

4pkl__assembly_2__model_1

4pkl__assembly_2__model_1 | I(q)

4pkl__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)