SAXSdb — 4d3i

▼

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

NITRIC OXIDE SYNTHASE OXYGENASE

BACILLUS SUBTILIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PROTOPORPHYRIN IX CONTAINING FE × 2 6,6'-{[5-(aminomethyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine) × 2 GLYCEROL × 2 N-PROPANOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOSO_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–363； UniProt 1–363

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4d3i
Deposition date deposition_date	2014-10-22
Structure title title	Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6,6'-((5-(aminomethyl)-1,3-phenylene)bis(ethane-2,1-diyl))bis(4- methylpyridin-2-amine)
Keywords keywords	NITRIC OXIDE SYNTHASE, OXIDOREDUCTASE, INHIBITOR; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4d3i__assembly_1__model_1

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

Download this curve (.dat)

4d3i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4d3i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.04 Å
Rg (electron density)	30.19 Å
Total Rg	30.97 Å
Atom count	6068
Residues	726
Excluded volume	107700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4d3i__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	NITRIC OXIDE SYNTHASE OXYGENASE
Molecular weight formula_weight	41787.1 kDa
EC 编号 ec_number	1.14.13.165
Mutation mutation	YES
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	3280

MEEKEILWNEAKAFIAACYQELGKAAEVKDRLADIKSEIDLTGSYVHTKEELEHGAKMAWRNSNRCIGRLFWNSLNVIDRRDVRTKEEVRDALFHHIETATNNGKIRPTITIFPPEEKGEKQVEIWNHQLIRYAGYESDGERIGDPASCSLTAACEELGWRGERTDFDLLPLIFRMKGDEQPVWYELPRSLVIEVPITHPDIEAFSDLELKWYGVPIISDMKLEVGGIHYNAAPFNGWYMGTEIGARNLADEKRYDKLKKVASVIGIAADYNTDLWKDQALVELNKAVLHSYKKQGVSIVDHHTAASQFKRFEEQAEEAGRKLTGDWTWLIPPISPAATHIFHRSYDNSIVKPNYFYQDKPYE

Source Source

Source organism organism	BACILLUS SUBTILIS
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	6,6'-{[5-(aminomethyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine)
Molecular weight formula_weight	375.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	N-PROPANOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	246

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4d3ia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.174 — Nitric oxide (NO) synthase oxygenase domain
Superfamily Superfamily superfamily	d.174.1 — Nitric oxide (NO) synthase oxygenase domain
Family Family family	d.174.1.1 — Nitric oxide (NO) synthase oxygenase domain

CATH v4.4 (3 domains)

Domain ID domain_id	4d3iA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	340 — Nitric Oxide Synthase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Nitric Oxide Synthase; Chain A, domain 1

Domain ID domain_id	4d3iA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2

Domain ID domain_id	4d3iA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
Homologous superfamily homologous superfamily	10 — Nitric Oxide Synthase; Chain A, domain 3

▶

Unit-cell length a length_a	80.510 Å
Unit-cell length b length_b	94.940 Å
Unit-cell length c length_c	63.490 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	44.138 Å
R factor r_factor	0.1700
R_work r_work	0.1674
R_free r_free	0.2199

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6,6'-((5-(aminomethyl)-1,3-phenylene)bis(ethane-2,1-diyl))bis(4- methylpyridin-2-amine)

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

NITRIC OXIDE SYNTHASE OXYGENASE

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

4d3i__assembly_1__model_1

4d3i__assembly_1__model_1 | I(q)

4d3i__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6,6'-((5-(aminomethyl)-1,3-phenylene)bis(ethane-2,1-diyl))bis(4- methylpyridin-2-amine)

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

NITRIC OXIDE SYNTHASE OXYGENASE

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

4d3i__assembly_1__model_1

4d3i__assembly_1__model_1 | I(q)

4d3i__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)