SAXSdb — 5j8d

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

Oxygen-insensitive NAD(P)H nitroreductase

Enterobacter cloacae

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 NICOTINIC ACID ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 NICOTINIC ACID ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NFSB_ENTCL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–216； UniProt 2–217 Author chain B； PDBConstruct 1–216； UniProt 2–217 Author chain C； PDBConstruct 1–216； UniProt 2–217 Author chain D； PDBConstruct 1–216； UniProt 2–217

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	5j8d
Deposition date deposition_date	2016-04-07
Structure title title	Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide
Keywords keywords	Nitroreductase, Complex, NAAD, Substrate, 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.

5j8d__assembly_1__model_1

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

Download this curve (.dat)

5j8d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5j8d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.99 Å
Rg (electron density)	20.76 Å
Total Rg	21.68 Å
Atom count	3504
Residues	432
Excluded volume	61818 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j8d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5j8d__assembly_2__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	Oxygen-insensitive NAD(P)H nitroreductase
Molecular weight formula_weight	23851.0 kDa
EC 编号 ec_number	1.-.-.-
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	8032

DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC

Source Source

Source organism organism	Enterobacter cloacae
NCBI taxonomy ID ncbi_taxonomy_id	550
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	4

Entity 3 Entity 3 non-polymer

Description description	NICOTINIC ACID ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1024

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5j8da_
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	d5j8db_
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	d5j8dc_
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	d5j8dd_
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 (4 domains)

Domain ID domain_id	5j8dA00
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	5j8dB00
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	5j8dC00
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	5j8dD00
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	49.380 Å
Unit-cell length b length_b	113.140 Å
Unit-cell length c length_c	80.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	19.842 Å
R factor r_factor	0.1780
R_work r_work	0.1747
R_free r_free	0.2124

Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide

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

Oxygen-insensitive NAD(P)H nitroreductase

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

5j8d__assembly_1__model_1

5j8d__assembly_1__model_1 | I(q)

5j8d__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide

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

Oxygen-insensitive NAD(P)H nitroreductase

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

5j8d__assembly_1__model_1

5j8d__assembly_1__model_1 | I(q)

5j8d__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)