SAXSdb — 3c9u

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

Thiamine monophosphate kinase

Aquifex aeolicus

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 × 10 THIAMINE DIPHOSPHATE × 2 ADENOSINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O67883_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 37–342； UniProt 1–306 Author chain B； PDBConstruct 37–342； UniProt 1–306

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	3c9u
Deposition date deposition_date	2008-02-18
Structure title title	AaThiL complexed with ADP and TPP
Keywords keywords	beta barrel, alpha-beta structure, Kinase, 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.

3c9u__assembly_1__model_1

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

Download this curve (.dat)

3c9u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c9u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.60 Å
Rg (electron density)	26.00 Å
Total Rg	26.77 Å
Atom count	5022
Residues	620
Excluded volume	89811 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c9u__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 (5)

Entity 1 Entity 1 polymer

Description description	Thiamine monophosphate kinase
Molecular weight formula_weight	38469.9 kDa
EC 编号 ec_number	2.7.4.16
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	5569

MGSHHHHHHDITSLYKKAGSAAAVLEENLYFQGSFTMRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEPKGWKHF

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

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	10

Entity 3 Entity 3 non-polymer

Description description	THIAMINE DIPHOSPHATE
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 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	547

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3c9ua1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d3c9ua2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

Domain ID domain_id	d3c9ua3
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	d3c9ub1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d3c9ub2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

Domain ID domain_id	d3c9ub3
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

CATH v4.4 (4 domains)

Domain ID domain_id	3c9uA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	3c9uA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

Domain ID domain_id	3c9uB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	3c9uB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

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Unit-cell length a length_a	60.573 Å
Unit-cell length b length_b	66.221 Å
Unit-cell length c length_c	196.990 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	1.480 Å
Low-resolution limit resolution_low	39.520 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2190

AaThiL complexed with ADP and TPP

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

Thiamine monophosphate 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

3c9u__assembly_1__model_1

3c9u__assembly_1__model_1 | I(q)

3c9u__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 (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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

AaThiL complexed with ADP and TPP

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

Thiamine monophosphate 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

3c9u__assembly_1__model_1

3c9u__assembly_1__model_1 | I(q)

3c9u__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 (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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)