SAXSdb — 2vf0

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

THYMIDYLATE SYNTHASE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE ; × 2 S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID × 2 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TYSY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 1–264 Author chain B； PDBConstruct 1–264； UniProt 1–264

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	2vf0
Deposition date deposition_date	2007-10-27
Structure title title	CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH 5NO2DUMP AND BW1843U89
Keywords keywords	;NUCLEOTIDE BIOSYNTHESIS, SUBSTRATE ANOLOGUE, ANTIFOLATE BINDING, RNA-BINDING, TRANSFERASE, METHYLTRANSFERASE, REPRESSOR, BW1843U89, CYTOPLASM, 5-NO2-DUMP, THYMIDYLATE SYNTHASE, TRANSLATION REGULATION ;; 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.

2vf0__assembly_1__model_1

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

Download this curve (.dat)

2vf0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vf0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.35 Å
Rg (electron density)	23.04 Å
Total Rg	23.93 Å
Atom count	4431
Residues	526
Excluded volume	78162 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vf0__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	THYMIDYLATE SYNTHASE
Molecular weight formula_weight	30558.6 kDa
EC 编号 ec_number	2.1.1.45
Mutation mutation	YES
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	4474

MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTQRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	511693
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE ;
Molecular weight formula_weight	355.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID
Molecular weight formula_weight	500.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vf0a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

Domain ID domain_id	d2vf0b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (2 domains)

Domain ID domain_id	2vf0A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

Domain ID domain_id	2vf0B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

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Unit-cell length a length_a	127.160 Å
Unit-cell length b length_b	127.160 Å
Unit-cell length c length_c	67.950 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 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	33.980 Å
R factor r_factor	0.1800
R_work r_work	0.1800
R_free r_free	0.2390

CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH 5NO2DUMP AND BW1843U89

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

THYMIDYLATE SYNTHASE

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

2vf0__assembly_1__model_1

2vf0__assembly_1__model_1 | I(q)

2vf0__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH 5NO2DUMP AND BW1843U89

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

THYMIDYLATE SYNTHASE

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

2vf0__assembly_1__model_1

2vf0__assembly_1__model_1 | I(q)

2vf0__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)