SAXSdb — 6e0b

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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	5-methyl-7-(naphthalen-2-ylamino)-1H-[1,2,4]triazolo[1,5-a]pyrimidine-3,8-diium × 1 FLAVIN MONONUCLEOTIDE × 1 OROTIC ACID × 1 GLYCEROL × 3 LAURYL DIMETHYLAMINE-N-OXIDE × 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 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	6e0b
Deposition date deposition_date	2018-07-06
Structure title title	Plasmodium falciparum dihydroorotate dehydrogenase C276F mutant bound with triazolopyrimidine-based inhibitor DSM1
Keywords keywords	;PLASMODIUM FALCIPARUM, DIHYDROOROTATE DEHYDROGENASE, TRIAZOLOPYRIMIDINE, INHIBITOR, DSM1, FAD, FLAVOPROTEIN, MEMBRANE, MITOCHONDRION, MITOCHONDRION INNER MEMBRANE, OXIDOREDUCTASE, PYRIMIDINE BIOSYNTHESIS, TRANSIT PEPTIDE ;; 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.

6e0b__assembly_1__model_1

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

Download this curve (.dat)

6e0b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6e0b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.69 Å
Rg (electron density)	19.66 Å
Total Rg	20.63 Å
Atom count	6166
Residues	375
Excluded volume	55141 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6e0b__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Dihydroorotate dehydrogenase (quinone), mitochondrial
Molecular weight formula_weight	45429.9 kDa
EC 编号 ec_number	1.3.5.2
Mutation mutation	C276F
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6280

MGHHHHHHAENLYFQGADPFESYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSFGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRKHSKS

Source Source

Source organism organism	Plasmodium falciparum
Common name common_name	isolate 3D7
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 non-polymer

Description description	5-methyl-7-(naphthalen-2-ylamino)-1H-[1,2,4]triazolo[1,5-a]pyrimidine-3,8-diium
Molecular weight formula_weight	277.3 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

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	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6e0bA00
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	85.522 Å
Unit-cell length b length_b	85.522 Å
Unit-cell length c length_c	138.879 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	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.099 Å
Low-resolution limit resolution_low	42.761 Å
R factor r_factor	0.1790
R_work r_work	0.1776
R_free r_free	0.2050

Plasmodium falciparum dihydroorotate dehydrogenase C276F mutant bound with triazolopyrimidine-based inhibitor DSM1

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

6e0b__assembly_1__model_1

6e0b__assembly_1__model_1 | I(q)

6e0b__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Plasmodium falciparum dihydroorotate dehydrogenase C276F mutant bound with triazolopyrimidine-based inhibitor DSM1

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

6e0b__assembly_1__model_1

6e0b__assembly_1__model_1 | I(q)

6e0b__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)