4fzb

Structure of thymidylate synthase ThyX complexed to a new inhibitor

Method: X-RAY DIFFRACTION

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

Probable thymidylate synthase

Paramecium bursaria Chlorella virus 1

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-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione × 4 DIMETHYL SULFOXIDE × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione × 4 DIMETHYL SULFOXIDE × 4 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione × 4 DIMETHYL SULFOXIDE × 2 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione × 4 DIMETHYL SULFOXIDE × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THYX_PBCV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–221； UniProt 2–216 Author chain B； PDBConstruct 7–221； UniProt 2–216 Author chain C； PDBConstruct 7–221； UniProt 2–216 Author chain D； PDBConstruct 7–221； UniProt 2–216 Author chain E； PDBConstruct 7–221； UniProt 2–216 Author chain F； PDBConstruct 7–221； UniProt 2–216 Author chain G； PDBConstruct 7–221； UniProt 2–216 Author chain H； PDBConstruct 7–221； UniProt 2–216 Author chain I； PDBConstruct 7–221； UniProt 2–216 Author chain J； PDBConstruct 7–221； UniProt 2–216 Author chain K； PDBConstruct 7–221； UniProt 2–216 Author chain L； PDBConstruct 7–221； UniProt 2–216 Author chain M； PDBConstruct 7–221； UniProt 2–216 Author chain N； PDBConstruct 7–221； UniProt 2–216 Author chain O； PDBConstruct 7–221； UniProt 2–216 Author chain P； PDBConstruct 7–221； UniProt 2–216

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	4fzb
Deposition date deposition_date	2012-07-06
Structure title title	Structure of thymidylate synthase ThyX complexed to a new inhibitor
Keywords keywords	Homotetramer, FAD-dependent Thymidylate synthase, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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.

4fzb__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4fzb__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4fzb__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	27.93 Å
Rg (electron density)	27.29 Å
Total Rg	28.08 Å
Atom count	6563
Residues	774
Excluded volume	116160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4fzb__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4fzb__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4fzb__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4fzb__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	Probable thymidylate synthase
Molecular weight formula_weight	26212.8 kDa
EC 编号 ec_number	2.1.1.148
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	26503

MASMTGSAKLISVTKPVVEGVNTAEELIAYAARVSNPENQINNKTASGLLKYCIRHKHWSIFETAFMTLELKTSRGIAAQVLRHRSFHFQEFSQRYASVMETPPPHQARFQDHKNRQNSLDTVPEDDQTWWATEQEKLYAQSMELYNKALEKGIAKECARFILPLSTPTTIYMSGTIRDWIHYIELRTSNGTQREHIDLANACKEIFIKEFPSIAKALDWVHHHHHH

Source Source

Source organism organism	Paramecium bursaria Chlorella virus 1
Common name common_name	PBCV-1
NCBI taxonomy ID ncbi_taxonomy_id	10506
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	16

Entity 3 Entity 3 non-polymer

Description description	2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione
Molecular weight formula_weight	294.3 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	92

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6. Fold Classification (SCOP + CATH) 32 domains

CATH v4.4 (32 domains)

Domain ID domain_id	4fzbA01
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	4fzbA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbB01
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	4fzbB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbC01
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	4fzbC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbD01
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	4fzbD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbE01
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	4fzbE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbF01
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	4fzbF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbG01
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	4fzbG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbH01
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	4fzbH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbI01
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	4fzbI02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbJ01
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	4fzbJ02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbK01
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	4fzbK02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbL01
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	4fzbL02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbM01
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	4fzbM02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbN01
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	4fzbN02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbO01
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	4fzbO02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	4fzbP01
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	4fzbP02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

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Unit-cell length a length_a	69.975 Å
Unit-cell length b length_b	120.585 Å
Unit-cell length c length_c	128.249 Å
Unit-cell angle α angle_alpha	111.65 °
Unit-cell angle β angle_beta	91.13 °
Unit-cell angle γ angle_gamma	90.18 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	34.210 Å
R factor r_factor	0.2132
R_work r_work	0.2106
R_free r_free	0.2613

Structure of thymidylate synthase ThyX complexed to a new inhibitor

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

Probable 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

4fzb__assembly_3__model_1

4fzb__assembly_3__model_1 | I(q)

4fzb__assembly_3__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) 32 domains

CATH v4.4 (32 domains)

7. Citations (1)

Structure of thymidylate synthase ThyX complexed to a new inhibitor

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

Probable 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

4fzb__assembly_3__model_1

4fzb__assembly_3__model_1 | I(q)

4fzb__assembly_3__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) 32 domains

CATH v4.4 (32 domains)

7. Citations (1)