SAXSdb — 3gz3

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

Dihydroorotate dehydrogenase, putative

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 OROTIC ACID × 2 GLYCEROL × 4 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	3gz3
Deposition date deposition_date	2009-04-06
Structure title title	Leishmania major Dihydroorotate Dehydrogenase in complex with orotate
Keywords keywords	orotate, DHODH, 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.

3gz3__assembly_1__model_1

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

Download this curve (.dat)

3gz3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gz3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.83 Å
Rg (electron density)	24.91 Å
Total Rg	25.72 Å
Atom count	4662
Residues	598
Excluded volume	83304 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gz3__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 (5)

Entity 1 Entity 1 polymer

Description description	Dihydroorotate dehydrogenase, putative
Molecular weight formula_weight	38159.5 kDa
EC 编号 ec_number	1.3.3.1
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	5128

MGSSHHHHHHSSGLVPAGSHMASMTGGQQMGRGSMSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTLDGTAESTR

Source Source

Source organism organism	Leishmania major
NCBI taxonomy ID ncbi_taxonomy_id	5664
Host organism host_organism	Escherichia coli

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	OROTIC ACID
Molecular weight formula_weight	156.1 kDa
Source method src_method	syn
Copy count entity_count	2

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	430

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3gz3a_
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	d3gz3b_
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

CATH v4.4 (4 domains)

Domain ID domain_id	3gz3A01
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	3gz3A02
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	3gz3B01
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	3gz3B02
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	142.167 Å
Unit-cell length b length_b	142.167 Å
Unit-cell length c length_c	69.157 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	30.000 Å
R factor r_factor	0.1781
R_work r_work	0.1767
R_free r_free	0.2042

Leishmania major Dihydroorotate Dehydrogenase in complex with orotate

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

Dihydroorotate dehydrogenase, putative

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

3gz3__assembly_1__model_1

3gz3__assembly_1__model_1 | I(q)

3gz3__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 (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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Leishmania major Dihydroorotate Dehydrogenase in complex with orotate

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

Dihydroorotate dehydrogenase, putative

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

3gz3__assembly_1__model_1

3gz3__assembly_1__model_1 | I(q)

3gz3__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 (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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)