SAXSdb — 2tsr

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

THYMIDYLATE SYNTHASE

Rattus norvegicus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TYSY_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–307； UniProt 1–307 Author chain B； PDBConstruct 1–307； UniProt 1–307 Author chain C； PDBConstruct 1–307； UniProt 1–307 Author chain D； PDBConstruct 1–307； UniProt 1–307

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	2tsr
Deposition date deposition_date	1998-06-19
Structure title title	THYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX
Keywords keywords	THYMIDYLATE SYNTHASE, METHYLTRANSFERASE, DUMP, TOMUDEX, ANTIFOLATE; METHYLTRANSFERASE
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.

2tsr__assembly_2__model_1

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

Download this curve (.dat)

2tsr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2tsr__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.79 Å
Rg (electron density)	23.51 Å
Total Rg	24.47 Å
Atom count	4646
Residues	562
Excluded volume	82465 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2tsr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2tsr__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	THYMIDYLATE SYNTHASE
Molecular weight formula_weight	35060.0 kDa
EC 编号 ec_number	2.1.1.45
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	9367

MLVEGSELQSGAQQPRTEAPQHGELQYLRQVEHIMRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSARQEGDLGPVYGFQWRHFGADYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVETIDDFKVEDFQIEGYNPHPTIKMEMAV

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 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 3 Entity 3 non-polymer

Description description	TOMUDEX
Molecular weight formula_weight	458.5 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	75

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2tsra_
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	d2tsrb_
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	d2tsrc_
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	d2tsrd_
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 (4 domains)

Domain ID domain_id	2tsrA00
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	2tsrB00
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	2tsrC00
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	2tsrD00
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	99.700 Å
Unit-cell length b length_b	101.600 Å
Unit-cell length c length_c	140.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1620
R_work r_work	0.1620
R_free r_free	0.2220

THYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX

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

2tsr__assembly_2__model_1

2tsr__assembly_2__model_1 | I(q)

2tsr__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

THYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX

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

2tsr__assembly_2__model_1

2tsr__assembly_2__model_1 | I(q)

2tsr__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)