3c61

Crystal structure of dihydroorotate dehydrogenase from Leishmania donovani

Method: X-RAY DIFFRACTION

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count
2	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count

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	3c61
Deposition date deposition_date	2008-02-01
Structure title title	Crystal structure of dihydroorotate dehydrogenase from Leishmania donovani
Keywords keywords	;STRUCTURAL GENOMICS, dihydroorotate dehydrogenase, leishmaniasis, OXIDOREDUCTASE, PSI, Protein Structure Initiative, Structural Genomics of Pathogenic Protozoa Consortium, SGPP ;; 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.

3c61__assembly_2__model_1

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

Download this curve (.dat)

3c61__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c61__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.81 Å
Rg (electron density)	24.85 Å
Total Rg	25.69 Å
Atom count	4870
Residues	628
Excluded volume	86783 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c61__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c61__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 (8)

Entity 1 Entity 1 polymer

Description description	Dihydroorotate dehydrogenase
Molecular weight formula_weight	34008.9 kDa
EC 编号 ec_number	1.3.99.11
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	10785

TMSLQVDLLNNTFANPFMNAAGVMCSTTEDLVAMTESASGSLVSKSCTPALREGNPTPRYRALPLGSINSMGLPNNGFDFYLAYAAEQHDYGRKPLFLSMSGLSVRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPQVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANVNAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALHEEGPAIFERLTAELLDVMAKKGYQTLDEFRGKVRTLD

Source Source

Source organism organism	Leishmania donovani
NCBI taxonomy ID ncbi_taxonomy_id	5661
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	OROTIC ACID
Molecular weight formula_weight	156.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	752

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3c61a1
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	d3c61a2
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	d3c61b1
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	d3c61b2
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	d3c61c1
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	d3c61c2
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	d3c61d1
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	d3c61d2
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	3c61A01
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	3c61A02
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	3c61B01
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	3c61B02
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	3c61C01
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	3c61C02
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	3c61D01
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	3c61D02
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	83.869 Å
Unit-cell length b length_b	83.869 Å
Unit-cell length c length_c	188.725 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 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	33.880 Å
R factor r_factor	0.1680
R_work r_work	0.1660
R_free r_free	0.1960