SAXSdb — 1v5y

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

Major NAD(P)H-flavin oxidoreductase

Aliivibrio fischeri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 4-HYDROXY-2H-CHROMEN-2-ONE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FRA1_VIBFI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–217； UniProt 1–217 Author chain B； PDBConstruct 1–217； UniProt 1–217

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	1v5y
Deposition date deposition_date	2003-11-26
Structure title title	Binding of coumarins to NAD(P)H:FMN oxidoreductase
Keywords keywords	coumarin, FMN oxidoreductase, inhibitor, 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.

1v5y__assembly_1__model_1

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

Download this curve (.dat)

1v5y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1v5y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.31 Å
Rg (electron density)	21.12 Å
Total Rg	22.01 Å
Atom count	3554
Residues	434
Excluded volume	62835 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1v5y__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 (4)

Entity 1 Entity 1 polymer

Description description	Major NAD(P)H-flavin oxidoreductase
Molecular weight formula_weight	24624.8 kDa
EC 编号 ec_number	1.6.99.-
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	3717

THPIIHDLENRYTSKKYDPSKKVSQEDLAVLLEALRLSASSINSQPWKFIVIESDAAKQRMHDSFANMHQFNQPHIKACSHVILFANKLSYTRDDYDVVLSKAVADKRITEEQKEAAFASFKFVELNCDENGEHKAWTKPQAYLALGNALHTLARLNIDSTTMEGIDPELLSEIFADELKGYECHVALAIGYHHPSEDYNASLPKSRKAFEDVITIL

Source Source

Source organism organism	Aliivibrio fischeri
NCBI taxonomy ID ncbi_taxonomy_id	668
Host organism host_organism	Escherichia coli

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	4-HYDROXY-2H-CHROMEN-2-ONE
Molecular weight formula_weight	162.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	163

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1v5ya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.90 — FMN-dependent nitroreductase-like
Superfamily Superfamily superfamily	d.90.1 — FMN-dependent nitroreductase-like
Family Family family	d.90.1.1 — NADH oxidase/flavin reductase

Domain ID domain_id	d1v5yb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.90 — FMN-dependent nitroreductase-like
Superfamily Superfamily superfamily	d.90.1 — FMN-dependent nitroreductase-like
Family Family family	d.90.1.1 — NADH oxidase/flavin reductase

CATH v4.4 (2 domains)

Domain ID domain_id	1v5yA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

Domain ID domain_id	1v5yB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

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Unit-cell length a length_a	101.600 Å
Unit-cell length b length_b	63.300 Å
Unit-cell length c length_c	74.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2260

Binding of coumarins to NAD(P)H:FMN oxidoreductase

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

Major NAD(P)H-flavin oxidoreductase

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

1v5y__assembly_1__model_1

1v5y__assembly_1__model_1 | I(q)

1v5y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Binding of coumarins to NAD(P)H:FMN oxidoreductase

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

Major NAD(P)H-flavin oxidoreductase

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

1v5y__assembly_1__model_1

1v5y__assembly_1__model_1 | I(q)

1v5y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)