SAXSdb — 5iot

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

Thymidylate synthase ThyX

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THYX_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–232； UniProt 1–220 Author chain B； PDBConstruct 13–232； UniProt 1–220 Author chain C； PDBConstruct 13–232； UniProt 1–220 Author chain D； PDBConstruct 13–232； UniProt 1–220

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	5iot
Deposition date deposition_date	2016-03-08
Structure title title	Flavin-dependent thymidylate synthase R174A variant in complex with FAD and dUMP
Keywords keywords	FAD-dependent, nucleotide biosynthesis, reductive methylation, 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.

5iot__assembly_1__model_1

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

Download this curve (.dat)

5iot__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5iot__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.83 Å
Rg (electron density)	28.42 Å
Total Rg	29.21 Å
Atom count	7460
Residues	863
Excluded volume	132870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5iot__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 (4)

Entity 1 Entity 1 polymer

Description description	Thymidylate synthase ThyX
Molecular weight formula_weight	27417.6 kDa
EC 编号 ec_number	2.1.1.148
Mutation mutation	R174A
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	7739

MGSDKIHHHHHHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLAADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV

Source Source

Source organism organism	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
Molecular weight formula_weight	308.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	263

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5iota_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
Superfamily Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
Family Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

Domain ID domain_id	d5iotb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
Superfamily Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
Family Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

Domain ID domain_id	d5iotb2
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	d5iotc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
Superfamily Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
Family Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

Domain ID domain_id	d5iotd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
Superfamily Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
Family Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

CATH v4.4 (4 domains)

Domain ID domain_id	5iotA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	5iotB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	5iotC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	5iotD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	170 —

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Unit-cell length a length_a	54.060 Å
Unit-cell length b length_b	115.860 Å
Unit-cell length c length_c	141.100 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	89.540 Å
R factor r_factor	0.1845
R_work r_work	0.1828
R_free r_free	0.2174

Flavin-dependent thymidylate synthase R174A variant in complex with FAD and dUMP

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

Thymidylate synthase ThyX

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

5iot__assembly_1__model_1

5iot__assembly_1__model_1 | I(q)

5iot__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Flavin-dependent thymidylate synthase R174A variant in complex with FAD and dUMP

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

Thymidylate synthase ThyX

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

5iot__assembly_1__model_1

5iot__assembly_1__model_1 | I(q)

5iot__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)