SAXSdb — 9tlz

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

Dihydroorotate dehydrogenase (quinone), mitochondrial

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FLAVIN MONONUCLEOTIDE × 1 OROTIC ACID × 1 1-methyl-3-oxidanyl-5-[[[3-[pentakis(fluoranyl)-$l^{6}-sulfanyl]phenyl]amino]methyl]pyrazole-4-carboxylic acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN MONONUCLEOTIDE × 1 OROTIC ACID × 1 1-methyl-3-oxidanyl-5-[[[3-[pentakis(fluoranyl)-$l^{6}-sulfanyl]phenyl]amino]methyl]pyrazole-4-carboxylic acid × 1 water × 1	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 24–405； UniProt 158–569 Author chain B； PDBConstruct 24–405； 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	9tlz
Deposition date deposition_date	2025-12-11
Last revision last_revision	2026-04-01
Structure title title	Plasmodium falciparum dihydroorotate dehydrogenase in complex with 3-hydroxy-1-methyl pyrazole derivatives
Keywords keywords	;Malaria, Plasmodium falciparum, Pyrimidine biosynthesis, dihydroorotate dehydrogenase, structure-based drug design, inhibitors, 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.

9tlz__assembly_2__model_1

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

Download this curve (.dat)

9tlz__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9tlz__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.52 Å
Rg (electron density)	19.50 Å
Total Rg	20.43 Å
Atom count	3041
Residues	374
Excluded volume	54237 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9tlz__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9tlz__assembly_2__model_1`	monomeric （1）	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 (quinone), mitochondrial
Molecular weight formula_weight	45852.5 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	6144

MHHHHHHSSGVDLGTENLYFQSMFESYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRKHSKS

Source Source

Source organism organism	Plasmodium falciparum
Common name common_name	malaria parasite P. falciparum
NCBI taxonomy ID ncbi_taxonomy_id	5833
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	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	1-methyl-3-oxidanyl-5-[[[3-[pentakis(fluoranyl)-$l^{6}-sulfanyl]phenyl]amino]methyl]pyrazole-4-carboxylic acid
Molecular weight formula_weight	373.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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Unit-cell length a length_a	52.364 Å
Unit-cell length b length_b	163.130 Å
Unit-cell length c length_c	62.656 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	48.130 Å
R factor r_factor	0.1934
R_work r_work	0.1898
R_free r_free	0.2613

Plasmodium falciparum dihydroorotate dehydrogenase in complex with 3-hydroxy-1-methyl pyrazole derivatives

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

9tlz__assembly_2__model_1

9tlz__assembly_2__model_1 | I(q)

9tlz__assembly_2__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

7. Citations (1)

Plasmodium falciparum dihydroorotate dehydrogenase in complex with 3-hydroxy-1-methyl pyrazole derivatives

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

9tlz__assembly_2__model_1

9tlz__assembly_2__model_1 | I(q)

9tlz__assembly_2__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

7. Citations (1)