5xfw

Crystal structures of FMN-free form of dihydroorotate dehydrogenase from Trypanosoma brucei

Method: X-RAY DIFFRACTION

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

Dihydroorotate dehydrogenase (fumarate)

Trypanosoma brucei brucei (strain 927/4 GUTat10.1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MALONATE ION × 8 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MALONATE ION × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRD_TRYB2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–334； UniProt 1–313 Author chain B； PDBConstruct 22–334； UniProt 1–313 Author chain C； PDBConstruct 22–334； UniProt 1–313 Author chain D； PDBConstruct 22–334； UniProt 1–313

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	5xfw
Deposition date deposition_date	2017-04-11
Structure title title	Crystal structures of FMN-free form of dihydroorotate dehydrogenase from Trypanosoma brucei
Keywords keywords	Neglected Tropical Diseases Flavin Enzyme Pyrimidine metabolism, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

5xfw__assembly_1__model_1

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

Download this curve (.dat)

5xfw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xfw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.97 Å
Rg (electron density)	25.07 Å
Total Rg	25.95 Å
Atom count	4850
Residues	626
Excluded volume	86946 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xfw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5xfw__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 (3)

Entity 1 Entity 1 polymer

Description description	Dihydroorotate dehydrogenase (fumarate)
Molecular weight formula_weight	36463.9 kDa
EC 编号 ec_number	1.3.98.1
Mutation mutation	A115V
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	10474

MAHHHHHHSAALEVLFQGPGSMSLKVNILGHEFSNPFMNAAGVLCTTEEDLRRMTESESGSLIGKSCTLAPRTGNPEPRYFGLPLGSINSMGLPNLGVDFYLSYAAQTHDYSRKPLFLSMSGLSVEESVEMVKKLVPITKEKGTILELNLSCPNVPGKPQVGYDFDTTRTYLQKVSEAYGLPFGVKMPPYFDIAHFDMAAAVLNDFPLVKFITCVNSIGNGLVIDPANETVVIKPKQGFGGLGGKYVLPTALANVNAFFRRCPDKLVFGCGGVYSGEEAFLHILAGASMVQVGTALHDEGPIIFARLNKELQEIMTNKGYKTLDEFRGRVKTMD

Source Source

Source organism organism	Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
NCBI taxonomy ID ncbi_taxonomy_id	185431
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	780

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5xfwa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.0 — automated matches

Domain ID domain_id	d5xfwb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.0 — automated matches

Domain ID domain_id	d5xfwc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.0 — automated matches

Domain ID domain_id	d5xfwd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.0 — automated matches

Domain ID domain_id	d5xfwd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	5xfwA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5xfwA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	26 — Dihydroorotate Dehydrogenase A; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Dihydroorotate Dehydrogenase A, chain A, domain 2

Domain ID domain_id	5xfwB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5xfwB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	26 — Dihydroorotate Dehydrogenase A; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Dihydroorotate Dehydrogenase A, chain A, domain 2

Domain ID domain_id	5xfwC01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5xfwC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	26 — Dihydroorotate Dehydrogenase A; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Dihydroorotate Dehydrogenase A, chain A, domain 2

Domain ID domain_id	5xfwD01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5xfwD02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	26 — Dihydroorotate Dehydrogenase A; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Dihydroorotate Dehydrogenase A, chain A, domain 2

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Unit-cell length a length_a	140.053 Å
Unit-cell length b length_b	146.218 Å
Unit-cell length c length_c	66.389 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	36.950 Å
R factor r_factor	0.1754
R_work r_work	0.1745
R_free r_free	0.1931

Crystal structures of FMN-free form of dihydroorotate dehydrogenase from Trypanosoma brucei

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

Dihydroorotate dehydrogenase (fumarate)

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

5xfw__assembly_1__model_1

5xfw__assembly_1__model_1 | I(q)

5xfw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structures of FMN-free form of dihydroorotate dehydrogenase from Trypanosoma brucei

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

Dihydroorotate dehydrogenase (fumarate)

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

5xfw__assembly_1__model_1

5xfw__assembly_1__model_1 | I(q)

5xfw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

CATH v4.4 (8 domains)

7. Citations (1)