3cl9

Structure of bifunctional TcDHFR-TS in complex with MTX

Method: X-RAY DIFFRACTION

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

Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS)

Trypanosoma cruzi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 CHLORIDE ION × 6 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 METHOTREXATE × 2 ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; × 2 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 CHLORIDE ION × 6 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 METHOTREXATE × 2 ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; × 2 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 8 CHLORIDE ION × 12 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 METHOTREXATE × 4 ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; × 4 1,2-ETHANEDIOL × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DRTS_TRYCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–521； UniProt 1–521

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	3cl9
Deposition date deposition_date	2008-03-18
Structure title title	Structure of bifunctional TcDHFR-TS in complex with MTX
Keywords keywords	;Bifunctional Enzyme in Complex with NADP, MTX and DUMP, Methyltransferase, Multifunctional enzyme, Nucleotide biosynthesis, One-carbon metabolism, Oxidoreductase, Transferase, OXIDOREDUCTASE-TRANSFERASE COMPLEX ;; OXIDOREDUCTASE, 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.

3cl9__assembly_2__model_1

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

Download this curve (.dat)

3cl9__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cl9__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.99 Å
Rg (electron density)	35.19 Å
Total Rg	35.63 Å
Atom count	8274
Residues	1010
Excluded volume	146220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cl9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cl9__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3cl9__assembly_3__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 (8)

Entity 1 Entity 1 polymer

Description description	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS)
Molecular weight formula_weight	58904.1 kDa
EC 编号 ec_number	1.5.1.3, 2.1.1.45
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4157

MSLFKIRMPETVAEGTRLALRAFSLVVAVDERGGIGDGRSIPWNVPEDMKFFRDVTTKLRGKNVKPSPAKRNAVVMGRKTWDSIPPKFRPLPGRLNVVLSSTLTTQHLLDGLPDEEKRNLHADSIVAVNGGLEQALQLLASPNYTPSIETVYCIGGGSVYAEALRPPCVHLLQAIYRTTIRASESSCSVFFRVPESGTEAAAGIEWQRETISEELTSANGNETKYYFEKLIPRNREEEQYLSLVDRIIREGNVKHDRTGVGTLSIFGAQMRFSLRNNRLPLLTTKRVFWRGVCEELLWFLRGETYAKKLSDKGVHIWDDNGSRAFLDSRGLTEYEEMDLGPVYGFQWRHFGAAYTHHDANYDGQGVDQIKAIVETLKTNPDDRRMLFTAWNPSALPRMALPPCHLLAQFYVSNGELSCMLYQRSCDMGLGVPFNIASYALLTILIAKATGLRPGELVHTLGDAHVYSNHVEPCNEQLKRVPRAFPYLVFRREREFLEDYEEGDMEVIDYAPYPPISMKMAV

Source Source

Source organism organism	Trypanosoma cruzi
NCBI taxonomy ID ncbi_taxonomy_id	5693
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	METHOTREXATE
Molecular weight formula_weight	454.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
Molecular weight formula_weight	308.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3cl9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	3cl9A02
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	121.050 Å
Unit-cell length b length_b	121.050 Å
Unit-cell length c length_c	260.760 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	19.780 Å
R factor r_factor	—
R_work r_work	0.2063
R_free r_free	0.2490

Structure of bifunctional TcDHFR-TS in complex with MTX

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

Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS)

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

3cl9__assembly_2__model_1

3cl9__assembly_2__model_1 | I(q)

3cl9__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of bifunctional TcDHFR-TS in complex with MTX

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

Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS)

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

3cl9__assembly_2__model_1

3cl9__assembly_2__model_1 | I(q)

3cl9__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)