SAXSdb — 4n09

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

Adenosine kinase

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	ADENOSINE × 1 ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ADENOSINE × 1 ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ADENOSINE × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ADENOSINE × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q584S0_TRYB2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–348； UniProt 1–345 Author chain B； PDBConstruct 4–348； UniProt 1–345 Author chain C； PDBConstruct 4–348； UniProt 1–345 Author chain D； PDBConstruct 4–348； UniProt 1–345

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	4n09
Deposition date deposition_date	2013-10-01
Structure title title	Structure of Trypanosoma brucei brucei adenosine kinase in complex with adenosine and AMPPNP
Keywords keywords	anion hole, adenosine kinase, adenosine, AMPPNP, TRANSFERASE; TRANSFERASE
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.

4n09__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4n09__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4n09__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	19.90 Å
Rg (electron density)	18.69 Å
Total Rg	19.52 Å
Atom count	2538
Residues	342
Excluded volume	44518 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4n09__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4n09__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4n09__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4n09__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	Adenosine kinase
Molecular weight formula_weight	38228.6 kDa
EC 编号 ec_number	2.7.1.20
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	10616

GPAMSSAPLRVYVQCNPLLDVSAHVSDEFLVKYGLERGTAILLSERQKGIFDDIEKMPNVRYVPGGSGLNVARVAQWMQQAYKGKFVTYVGCIADDRYGKVLKEAAEHEGIVMAVEHTTKAGSGACAVCITGKERTLVADLGAANHLSSEHMRSPAVVRAMDESRIFYFSGFTLTVDVNHVLQACRKAREVDGLFMINLSAPFIMQFFSAQLGEVLPYTDIIVANRHEAKEFANMMKWDTDCVEEIARRAVSEVPYTGTKGRVVVFTRDIESTVLATKDGVETVPVPQLDQDKVIDMNGAGDAFMGGFLSAYAVGKDLRRCCETGHYTAQEVIQRDGCSFPEKPSFSP

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	ADENOSINE
Molecular weight formula_weight	267.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4n09a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.0 — automated matches

Domain ID domain_id	d4n09b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.0 — automated matches

Domain ID domain_id	d4n09c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.0 — automated matches

Domain ID domain_id	d4n09d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	4n09A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	4n09A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n09B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	4n09B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n09C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	4n09C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n09D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	4n09D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	184.530 Å
Unit-cell length b length_b	90.220 Å
Unit-cell length c length_c	98.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.78 °
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	2.600 Å
Low-resolution limit resolution_low	65.040 Å
R factor r_factor	0.1880
R_work r_work	0.1862
R_free r_free	0.2214

Structure of Trypanosoma brucei brucei adenosine kinase in complex with adenosine and AMPPNP

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

Adenosine kinase

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

4n09__assembly_4__model_1

4n09__assembly_4__model_1 | I(q)

4n09__assembly_4__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of Trypanosoma brucei brucei adenosine kinase in complex with adenosine and AMPPNP

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

Adenosine kinase

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

4n09__assembly_4__model_1

4n09__assembly_4__model_1 | I(q)

4n09__assembly_4__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)