SAXSdb — 6vty

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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 monomer	Monomer	Protein 1	ethyl 3,5-dimethyl-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxylate × 1 FLAVIN MONONUCLEOTIDE × 1 OROTIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ethyl 3,5-dimethyl-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxylate × 1 FLAVIN MONONUCLEOTIDE × 1 OROTIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ethyl 3,5-dimethyl-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxylate × 1 FLAVIN MONONUCLEOTIDE × 1 OROTIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ethyl 3,5-dimethyl-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxylate × 1 FLAVIN MONONUCLEOTIDE × 1 OROTIC 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 20–431； UniProt 158–569 Author chain B； PDBConstruct 20–431； UniProt 158–569 Author chain C； PDBConstruct 20–431； UniProt 158–569 Author chain D； PDBConstruct 20–431； 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	6vty
Deposition date deposition_date	2020-02-13
Structure title title	Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM483
Keywords keywords	Oxidoreductase, mitochondria, alpha-beta barrel; 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.

6vty__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6vty__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6vty__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	20.34 Å
Rg (electron density)	19.34 Å
Total Rg	20.26 Å
Atom count	5987
Residues	368
Excluded volume	53561 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6vty__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6vty__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6vty__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6vty__assembly_4__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	48946.8 kDa
EC 编号 ec_number	1.3.5.2
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	25167

MGHHHHHHAENLYFQGADPFESYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDESTYNEDNKIVEKKNNFNKNNSHMMKDAKDNFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRKHSKS

Source Source

Source organism organism	Plasmodium falciparum (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	ethyl 3,5-dimethyl-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxylate
Molecular weight formula_weight	325.3 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	4

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	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	897

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6vtya1
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	d6vtya2
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	d6vtyb_
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	d6vtyc_
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	d6vtyd_
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	6vtyA00
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	6vtyB00
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	6vtyC00
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	6vtyD00
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	92.088 Å
Unit-cell length b length_b	97.521 Å
Unit-cell length c length_c	186.252 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	42.030 Å
R factor r_factor	—
R_work r_work	0.1514
R_free r_free	0.1939

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM483

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

6vty__assembly_4__model_1

6vty__assembly_4__model_1 | I(q)

6vty__assembly_4__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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM483

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

6vty__assembly_4__model_1

6vty__assembly_4__model_1 | I(q)

6vty__assembly_4__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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)