4q0d

Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP, methotrexate and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-L-glutamic acid.

Method: X-RAY DIFFRACTION

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

Bifunctional dihydrofolate reductase-thymidylate synthase

Cryptosporidium hominis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 N-{4-[(2-amino-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzoyl}-L-glutamic acid × 2 METHOTREXATE × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 N-{4-[(2-amino-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzoyl}-L-glutamic acid × 2 METHOTREXATE × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 N-{4-[(2-amino-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzoyl}-L-glutamic acid × 2 METHOTREXATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5CGA3_CRYHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–521； UniProt 1–521 Author chain B； PDBConstruct 1–521； UniProt 1–521 Author chain C； PDBConstruct 1–521； UniProt 1–521 Author chain D； PDBConstruct 1–521； UniProt 1–521 Author chain E； 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	4q0d
Deposition date deposition_date	2014-04-01
Structure title title	Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP, methotrexate and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-L-glutamic acid.
Keywords keywords	bifunctional enzyme, transferase, oxidoreductase, 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.

4q0d__assembly_3__model_1

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

Download this curve (.dat)

4q0d__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4q0d__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	33.52 Å
Rg (electron density)	32.44 Å
Total Rg	33.03 Å
Atom count	8538
Residues	1016
Excluded volume	151490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4q0d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4q0d__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4q0d__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	Bifunctional dihydrofolate reductase-thymidylate synthase
Molecular weight formula_weight	60262.5 kDa
EC 编号 ec_number	2.1.1.45, 1.5.1.3
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A,B,C,D
Atom count atom_count	21345

MSEKNVSIVVAASVLSSGIGINGQLPWSISEDLKFFSKITNNKCDSNKKNALIMGRKTWDSIGRRPLKNRIIVVISSSLPQDEADPNVVVFRNLEDSIENLMNDDSIENIFVCGGESIYRDALKDNFVDRIYLTRVALEDIEFDTYFPEIPETFLPVYMSQTFCTKNISYDFMIFEKQEKKTLQNCDPARGQLKSIDDTVDLLGEIFGIRKMGNRHKFPKEEIYNTPSIRFGREHYEFQYLDLLSRVLENGAYRENRTGISTYSIFGQMMRFDMRESFPLLTTKKVAIRSIFEELIWFIKGDTNGNHLIEKKVYIWSGNGSKEYLERIGLGHREENDLGPIYGFQWRHYNGEYKTMHDDYTGVGVDQLAKLIETLKNNPKDRRHILTAWNPSALSQMALPPCHVLSQYYVTNDNCLSCNLYQRSCDLGLGSPFNIASYAILTMMLAQVCGYEPGELAIFIGDAHIYENHLTQLKEQLSRTPRPFPQLKFKRKVENIEDFKWEDIELIGYYPYPTIKMDMAV

Source Source

Source organism organism	Cryptosporidium hominis
NCBI taxonomy ID ncbi_taxonomy_id	237895
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	326.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	N-{4-[(2-amino-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzoyl}-L-glutamic acid
Molecular weight formula_weight	413.4 kDa
Source method src_method	syn
Copy count entity_count	5

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	5

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6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id	4q0dA01
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	4q0dA02
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	4q0dA03
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	4q0dB01
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	4q0dB02
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	4q0dB03
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	4q0dC01
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	4q0dC02
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	4q0dC03
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	4q0dD01
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	4q0dD02
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	4q0dD03
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	4q0dE01
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	4q0dE02
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	4q0dE03
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	213.611 Å
Unit-cell length b length_b	115.031 Å
Unit-cell length c length_c	217.643 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

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

Resolution resolution	3.449 Å
Low-resolution limit resolution_low	48.941 Å
R factor r_factor	0.2181
R_work r_work	0.2173
R_free r_free	0.2420

Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP, methotrexate and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-L-glutamic acid.

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

Bifunctional dihydrofolate reductase-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

4q0d__assembly_3__model_1

4q0d__assembly_3__model_1 | I(q)

4q0d__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 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)

Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP, methotrexate and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-L-glutamic acid.

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

Bifunctional dihydrofolate reductase-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

4q0d__assembly_3__model_1

4q0d__assembly_3__model_1 | I(q)

4q0d__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 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)