SAXSdb — 1ig0

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

Thiamin pyrophosphokinase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THI80_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–319； UniProt 1–319 Author chain B； PDBConstruct 1–319； UniProt 1–319

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	1ig0
Deposition date deposition_date	2001-04-16
Structure title title	Crystal Structure of yeast Thiamin Pyrophosphokinase
Keywords keywords	Protein-substrate complex, compound active site, alpha-beta-alpha, beta sandwich, 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.

1ig0__assembly_1__model_1

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

Download this curve (.dat)

1ig0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ig0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.77 Å
Rg (electron density)	25.57 Å
Total Rg	26.45 Å
Atom count	5160
Residues	636
Excluded volume	92694 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ig0__assembly_1__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Thiamin pyrophosphokinase
Molecular weight formula_weight	36659.0 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	5830

MSEECIENPERIKIGTDLINIRNKMNLKELIHPNEDENSTLLILNQKIDIPRPLFYKIWKLHDLKVCADGAANRLYDYLDDDETLRIKYLPNYIIGDLDSLSEKVYKYYRKNKVTIIKQTTQYSTDFTKCVNLISLHFNSPEFRSLISNKDNLQSNHGIELEKGIHTLYNTMTESLVFSKVTPISLLALGGIGGRFDQTVHSITQLYTLSENASYFKLCYMTPTDLIFLIKKNGTLIEYDPQFRNTCIGNCGLLPIGEATLVKETRGLKWDVKNWPTSVVTGRVSSSNRFVGDNCCFIDTKDDIILNVEIFVDKLIDFL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
Molecular weight formula_weight	265.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	670

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ig0a1
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	d1ig0a2
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	d1ig0b1
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	d1ig0b2
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

CATH v4.4 (4 domains)

Domain ID domain_id	1ig0A01
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	1ig0A02
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	1ig0B01
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	1ig0B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	320 — Thiamin pyrophosphokinase, thiamin-binding domain

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Unit-cell length a length_a	118.313 Å
Unit-cell length b length_b	130.839 Å
Unit-cell length c length_c	44.319 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	29.460 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2340

Crystal Structure of yeast Thiamin Pyrophosphokinase

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

Thiamin pyrophosphokinase

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

1ig0__assembly_1__model_1

1ig0__assembly_1__model_1 | I(q)

1ig0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of yeast Thiamin Pyrophosphokinase

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

Thiamin pyrophosphokinase

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

1ig0__assembly_1__model_1

1ig0__assembly_1__model_1 | I(q)

1ig0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)