9qdk

Trypanosoma brucei PTR1 in complex with fragment L330 and compound F46

Method: X-RAY DIFFRACTION

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

Pteridine reductase

Trypanosoma brucei brucei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 2-amino-3H,4H,7H-pyrrolo[2,3-d]pyrimidin-4-one × 4 1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine × 4 ACETATE ION × 2 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O76290_TRYBB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–288； UniProt 1–268 Author chain B； PDBConstruct 21–288； UniProt 1–268 Author chain C； PDBConstruct 21–288； UniProt 1–268 Author chain D； PDBConstruct 21–288； UniProt 1–268

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	9qdk
Deposition date deposition_date	2025-03-06
Last revision last_revision	2026-03-18
Structure title title	Trypanosoma brucei PTR1 in complex with fragment L330 and compound F46
Keywords keywords	Trypanosoma brucei, pteridine reductase, PTR1, TbPTR1, fragment based drug design, NADPH, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

9qdk__assembly_1__model_1

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

Download this curve (.dat)

9qdk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qdk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.29 Å
Rg (electron density)	28.08 Å
Total Rg	28.76 Å
Atom count	7595
Residues	985
Excluded volume	134750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qdk__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 (7)

Entity 1 Entity 1 polymer

Description description	Pteridine reductase
Molecular weight formula_weight	30669.8 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	8336

MGSSHHHHHHSSGLVPRGSHMEAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA

Source Source

Source organism organism	Trypanosoma brucei brucei
NCBI taxonomy ID ncbi_taxonomy_id	5702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2-amino-3H,4H,7H-pyrrolo[2,3-d]pyrimidin-4-one
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine
Molecular weight formula_weight	292.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

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	627

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Unit-cell length a length_a	74.505 Å
Unit-cell length b length_b	89.298 Å
Unit-cell length c length_c	82.629 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	41.740 Å
R factor r_factor	0.1730
R_work r_work	0.1706
R_free r_free	0.2167

Trypanosoma brucei PTR1 in complex with fragment L330 and compound F46

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

Pteridine reductase

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

9qdk__assembly_1__model_1

9qdk__assembly_1__model_1 | I(q)

9qdk__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 (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

7. Citations (1)

Trypanosoma brucei PTR1 in complex with fragment L330 and compound F46

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

Pteridine reductase

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

9qdk__assembly_1__model_1

9qdk__assembly_1__model_1 | I(q)

9qdk__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 (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

7. Citations (1)