2af6

Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)

Method: X-RAY DIFFRACTION

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

Thymidylate synthase thyX

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	IODIDE ION × 5 FLAVIN-ADENINE DINUCLEOTIDE × 4 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 4 GLYCEROL × 8 water × 4	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 4 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 GLYCEROL × 5 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	IODIDE ION × 5 FLAVIN-ADENINE DINUCLEOTIDE × 4 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 4 GLYCEROL × 6 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 GLYCEROL × 3 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 3 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 GLYCEROL × 3 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 GLYCEROL × 4 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 3 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 GLYCEROL × 4 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 GLYCEROL × 3 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 GLYCEROL × 3 water × 2	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 3 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 GLYCEROL × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THYX_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–250； UniProt 1–250 Author chain B； PDBConstruct 1–250； UniProt 1–250 Author chain C； PDBConstruct 1–250； UniProt 1–250 Author chain D； PDBConstruct 1–250； UniProt 1–250 Author chain E； PDBConstruct 1–250； UniProt 1–250 Author chain F； PDBConstruct 1–250； UniProt 1–250 Author chain G； PDBConstruct 1–250； UniProt 1–250 Author chain H； PDBConstruct 1–250； UniProt 1–250

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	2af6
Deposition date deposition_date	2005-07-25
Structure title title	Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)
Keywords keywords	M.tuberculosis, ThyX, FDTS, TSCP, flavin dependent thymidylate synthase, 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.

2af6__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2af6__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2af6__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	27.17 Å
Rg (electron density)	26.44 Å
Total Rg	27.17 Å
Atom count	3932
Residues	479
Excluded volume	69128 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2af6__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2af6__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2af6__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2af6__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2af6__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2af6__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2af6__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2af6__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2af6__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`2af6__assembly_10__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 (6)

Entity 1 Entity 1 polymer

Description description	Thymidylate synthase thyX
Molecular weight formula_weight	28970.0 kDa
EC 编号 ec_number	2.1.1.148
Mutation mutation	I65M / L175M double mutant
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	16789

MAETAPLRVQLIAKTDFLAPPDVPWTTDADGGPALVEFAGRACYQSWSKPNPKTATNAGYLRHIMDVGHFSVLEHASVSFYITGISRSCTHELIRHRHFSYSQLSQRYVPEKDSRVVVPPGMEDDADLRHILTEAADAARATYSELLAKLEAKFADQPNAILRRKQARQAARAVMPNATETRIVVTGNYRAWRHFIAMRASEHADVEIRRLAIECLRQLAAVAPAVFADFEVTTLADGTEVATSPLATEALEHHHHHH

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	387.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	989

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	2af6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	2af6A02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2af6A03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2af6B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	2af6B02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2af6B03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2af6C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	2af6C02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2af6C03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2af6D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	2af6D02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2af6D03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2af6E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	2af6E02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2af6E03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2af6F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	2af6F02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2af6F03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2af6G01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	2af6G02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2af6G03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2af6H01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	2af6H02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2af6H03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

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Unit-cell length a length_a	81.090 Å
Unit-cell length b length_b	78.300 Å
Unit-cell length c length_c	168.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	44.950 Å
R factor r_factor	0.1978
R_work r_work	0.1955
R_free r_free	0.2429

Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)

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

2af6__assembly_6__model_1

2af6__assembly_6__model_1 | I(q)

2af6__assembly_6__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)

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

2af6__assembly_6__model_1

2af6__assembly_6__model_1 | I(q)

2af6__assembly_6__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)