SAXSdb — 2f17

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

Thiamin pyrophosphokinase 1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 SULFATE ION × 6 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM × 2 ADENOSINE MONOPHOSPHATE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 SULFATE ION × 12 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM × 4 ADENOSINE MONOPHOSPHATE × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TPK1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–263； UniProt 1–243 Author chain B； PDBConstruct 21–263； UniProt 1–243

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	2f17
Deposition date deposition_date	2005-11-14
Structure title title	Mouse Thiamin Pyrophosphokinase in a Ternary Complex with Pyrithiamin Pyrophosphate and AMP at 2.5 angstrom
Keywords keywords	BETA BARREL, ALPHA/BETA/ALPHA SANDWICH, pyrophosphokinase, AMP, 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.

2f17__assembly_2__model_1

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

Download this curve (.dat)

2f17__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f17__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	44.50 Å
Rg (electron density)	44.52 Å
Total Rg	44.81 Å
Atom count	8042
Residues	996
Excluded volume	142970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f17__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2f17__assembly_2__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	Thiamin pyrophosphokinase 1
Molecular weight formula_weight	29268.4 kDa
EC 编号 ec_number	2.7.6.2
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	4153

MGSSHHHHHHSSGLVPRGSHMEHAFTPLEPLLPTGNLKYCLVVLNQPLDARFRHLWKKALLRACADGGANHLYDLTEGERESFLPEFVSGDFDSIRPEVKEYYTKKGCDLISTPDQDHTDFTKCLQVLQRKIEEKELQVDVIVTLGGLGGRFDQIMASVNTLFQATHITPVPIIIIQKDSLIYLLQPGKHRLHVDTGMEGSWCGLIPVGQPCNQVTTTGLKWNLTNDVLGFGTLVSTSNTYDGSGLVTVETDHPLLWTMAIKS

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM
Molecular weight formula_weight	419.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 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	132

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2f17a1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.6 — Thiamin pyrophosphokinase, substrate-binding domain
Family Family family	b.82.6.1 — Thiamin pyrophosphokinase, substrate-binding domain

Domain ID domain_id	d2f17a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.100 — Thiamin pyrophosphokinase, catalytic domain
Superfamily Superfamily superfamily	c.100.1 — Thiamin pyrophosphokinase, catalytic domain
Family Family family	c.100.1.1 — Thiamin pyrophosphokinase, catalytic domain

Domain ID domain_id	d2f17a3
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	d2f17b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.100 — Thiamin pyrophosphokinase, catalytic domain
Superfamily Superfamily superfamily	c.100.1 — Thiamin pyrophosphokinase, catalytic domain
Family Family family	c.100.1.1 — Thiamin pyrophosphokinase, catalytic domain

Domain ID domain_id	d2f17b2
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.6 — Thiamin pyrophosphokinase, substrate-binding domain
Family Family family	b.82.6.1 — Thiamin pyrophosphokinase, substrate-binding domain

CATH v4.4 (4 domains)

Domain ID domain_id	2f17A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	320 — Thiamin pyrophosphokinase, thiamin-binding domain

Domain ID domain_id	2f17A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10240 — Thiamin pyrophosphokinase, catalytic domain

Domain ID domain_id	2f17B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	320 — Thiamin pyrophosphokinase, thiamin-binding domain

Domain ID domain_id	2f17B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10240 — Thiamin pyrophosphokinase, catalytic domain

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Unit-cell length a length_a	89.363 Å
Unit-cell length b length_b	89.363 Å
Unit-cell length c length_c	141.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2400
R_work r_work	0.2370
R_free r_free	0.2520

Mouse Thiamin Pyrophosphokinase in a Ternary Complex with Pyrithiamin Pyrophosphate and AMP at 2.5 angstrom

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

Thiamin pyrophosphokinase 1

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

2f17__assembly_2__model_1

2f17__assembly_2__model_1 | I(q)

2f17__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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Mouse Thiamin Pyrophosphokinase in a Ternary Complex with Pyrithiamin Pyrophosphate and AMP at 2.5 angstrom

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

Thiamin pyrophosphokinase 1

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

2f17__assembly_2__model_1

2f17__assembly_2__model_1 | I(q)

2f17__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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)