SAXSdb — 6dwg

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

Dihydroorotate dehydrogenase (fumarate)

Leishmania major

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 SULFATE ION × 3 GLYCEROL × 4 NICKEL (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4QEW7_LEIMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 35–354； UniProt 1–320 Author chain B； PDBConstruct 35–354； UniProt 1–320

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	6dwg
Deposition date deposition_date	2018-06-26
Structure title title	Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant Q139A
Keywords keywords	dihydroorotate dehydrogenase, Leishmania major, mutant Q139A, 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.

6dwg__assembly_1__model_1

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

Download this curve (.dat)

6dwg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6dwg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.90 Å
Rg (electron density)	24.98 Å
Total Rg	25.77 Å
Atom count	4691
Residues	613
Excluded volume	83902 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6dwg__assembly_1__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	Dihydroorotate dehydrogenase (fumarate)
Molecular weight formula_weight	38102.5 kDa
EC 编号 ec_number	1.3.98.1
Mutation mutation	Q139A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5301

MGSSHHHHHHSSGLVPAGSHMASMTGGQQMGRGSMSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPAVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTLDGTAESTR

Source Source

Source organism organism	Leishmania major
NCBI taxonomy ID ncbi_taxonomy_id	5664
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	382

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6dwga1
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.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d6dwga2
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

Domain ID domain_id	d6dwgb1
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.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d6dwgb2
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 (4 domains)

Domain ID domain_id	6dwgA01
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	6dwgA02
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	6dwgB01
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	6dwgB02
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	143.469 Å
Unit-cell length b length_b	143.469 Å
Unit-cell length c length_c	69.737 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	46.960 Å
R factor r_factor	0.1750
R_work r_work	0.1740
R_free r_free	0.1950

Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant Q139A

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

6dwg__assembly_1__model_1

6dwg__assembly_1__model_1 | I(q)

6dwg__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant Q139A

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

6dwg__assembly_1__model_1

6dwg__assembly_1__model_1 | I(q)

6dwg__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)