7s87

Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01

Method: X-RAY DIFFRACTION

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

Dihydroorotate dehydrogenase (quinone), mitochondrial

Plasmodium falciparum (isolate 3D7)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(4R)-3-methyl-5-[(4R)-4-methyl-3,4-dihydroisoquinolin-2(1H)-yl]thieno[2,3-e][1,2,4]triazolo[4,3-c]pyrimidine × 4 FLAVIN MONONUCLEOTIDE × 2 OROTIC ACID × 2 ACETATE ION × 1 polyethylene glycol × 1 SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRD_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–401； UniProt 158–569 Author chain B； PDBConstruct 20–401； UniProt 158–569

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	7s87
Deposition date deposition_date	2021-09-17
Structure title title	Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01
Keywords keywords	;inhibitor, DHODH, TIM Barrel, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, OXIDOREDUCTASE, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex ;; OXIDOREDUCTASE/OXIDOREDUCTASE 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.

7s87__assembly_1__model_1

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

Download this curve (.dat)

7s87__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7s87__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.78 Å
Rg (electron density)	31.28 Å
Total Rg	31.77 Å
Atom count	5876
Residues	752
Excluded volume	104790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7s87__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 (8)

Entity 1 Entity 1 polymer

Description description	Dihydroorotate dehydrogenase (quinone), mitochondrial
Molecular weight formula_weight	45385.9 kDa
EC 编号 ec_number	1.3.5.2
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	5964

MGHHHHHHAENLYFQGADPFESYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRKHSKS

Source Source

Source organism organism	Plasmodium falciparum (isolate 3D7)
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(4R)-3-methyl-5-[(4R)-4-methyl-3,4-dihydroisoquinolin-2(1H)-yl]thieno[2,3-e][1,2,4]triazolo[4,3-c]pyrimidine
Molecular weight formula_weight	335.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	polyethylene glycol
Molecular weight formula_weight	662.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	79

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7s87A01
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	7s87B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	124.726 Å
Unit-cell length b length_b	161.093 Å
Unit-cell length c length_c	92.569 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	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	orthorhombic

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	67.500 Å
R factor r_factor	0.1728
R_work r_work	0.1698
R_free r_free	0.2300

Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01

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

Dihydroorotate dehydrogenase (quinone), mitochondrial

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

7s87__assembly_1__model_1

7s87__assembly_1__model_1 | I(q)

7s87__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01

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

Dihydroorotate dehydrogenase (quinone), mitochondrial

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

7s87__assembly_1__model_1

7s87__assembly_1__model_1 | I(q)

7s87__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)