SAXSdb — 1f28

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

THYMIDYLATE SYNTHASE

Pneumocystis carinii

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 S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;2'-DEOXYURIDINE 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 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TYSY_PNECA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 1–297 Author chain B； PDBConstruct 1–297； UniProt 1–297 Author chain C； PDBConstruct 1–297； UniProt 1–297 Author chain D； PDBConstruct 1–297； UniProt 1–297

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	1f28
Deposition date deposition_date	2000-05-23
Structure title title	CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII BOUND TO DUMP AND BW1843U89
Keywords keywords	beta-sheet, protein-inhibitor complex, 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.

1f28__assembly_1__model_1

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

Download this curve (.dat)

1f28__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1f28__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.99 Å
Rg (electron density)	23.64 Å
Total Rg	24.53 Å
Atom count	4911
Residues	590
Excluded volume	87060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1f28__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1f28__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	34403.3 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	10322

MVNAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI

Source Source

Source organism organism	Pneumocystis carinii
NCBI taxonomy ID ncbi_taxonomy_id	4754
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	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	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	500

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1f28a_
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	d1f28b_
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	d1f28c_
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	d1f28d_
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	1f28A00
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	1f28B00
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	1f28C00
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	1f28D00
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	54.442 Å
Unit-cell length b length_b	65.898 Å
Unit-cell length c length_c	184.938 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	22.400 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2470

CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII BOUND TO DUMP 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

1f28__assembly_1__model_1

1f28__assembly_1__model_1 | I(q)

1f28__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII BOUND TO DUMP 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

1f28__assembly_1__model_1

1f28__assembly_1__model_1 | I(q)

1f28__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)