5uo8

Structure of human endothelial nitric oxide synthase heme domain in complex with 3-[(2-aminoquinolin-7-yl)methoxy]-5-((methylamino)methyl)benzonitrile

Method: X-RAY DIFFRACTION

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

Nitric oxide synthase, endothelial

Homo sapiens

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 5,6,7,8-TETRAHYDROBIOPTERIN × 2 3-[(2-aminoquinolin-7-yl)methoxy]-5-[(methylamino)methyl]benzonitrile × 2 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 ZINC ION × 1 GLYCEROL × 1 GADOLINIUM ATOM × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PROTOPORPHYRIN IX CONTAINING FE × 2 5,6,7,8-TETRAHYDROBIOPTERIN × 2 3-[(2-aminoquinolin-7-yl)methoxy]-5-[(methylamino)methyl]benzonitrile × 2 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 ZINC ION × 1 GLYCEROL × 1 GADOLINIUM ATOM × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOS3_HUMAN
Isoform	P29474-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–440； UniProt 41–480 Author chain B； PDBConstruct 1–440； UniProt 41–480 Author chain C； PDBConstruct 1–440； UniProt 41–480 Author chain D； PDBConstruct 1–440； UniProt 41–480

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	5uo8
Deposition date deposition_date	2017-01-31
Structure title title	Structure of human endothelial nitric oxide synthase heme domain in complex with 3-[(2-aminoquinolin-7-yl)methoxy]-5-((methylamino)methyl)benzonitrile
Keywords keywords	nitric, oxide, synthase, inhibitor, complex, heme, enzyme, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
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.

5uo8__assembly_1__model_1

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

Download this curve (.dat)

5uo8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5uo8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.22 Å
Rg (electron density)	29.31 Å
Total Rg	30.08 Å
Atom count	6670
Residues	806
Excluded volume	118230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5uo8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5uo8__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 (9)

Entity 1 Entity 1 polymer

Description description	Nitric oxide synthase, endothelial
Molecular weight formula_weight	49345.8 kDa
EC 编号 ec_number	1.14.13.39
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	13679

APASLLPPAPEHSPPSSPLTQPPEGPKFPRVKNWEVGSITYDTLSAQAQQDGPCTPRRCLGSLVFPRKLQGRPSPGPPAPEQLLSQARDFINQYYSSIKRSGSQAHEQRLQEVEAEVAATGTYQLRESELVFGAKQAWRNAPRCVGRIQWGKLQVFDARDCRSAQEMFTYICNHIKYATNRGNLRSAITVFPQRCPGRGDFRIWNSQLVRYAGYRQQDGSVRGDPANVEITELCIQHGWTPGNGRFDVLPLLLQAPDEPPELFLLPPELVLEVPLEHPTLEWFAALGLRWYALPAVSNMLLEIGGLEFPAAPFSGWYMSTEIGTRNLCDPHRYNILEDVAVCMDLDTRTTSSLWKDKAAVEINVAVLHSYQLAKVTIVDHHAATASFMKHLENEQKARGGCPADWAWIVPPISGSLTPVFHQEMVNYFLSPAFRYQPDPW

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

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	4

Entity 3 Entity 3 non-polymer

Description description	5,6,7,8-TETRAHYDROBIOPTERIN
Molecular weight formula_weight	241.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	3-[(2-aminoquinolin-7-yl)methoxy]-5-[(methylamino)methyl]benzonitrile
Molecular weight formula_weight	318.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	GADOLINIUM ATOM
Molecular weight formula_weight	157.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	325

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5uo8a_
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

Domain ID domain_id	d5uo8b_
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

Domain ID domain_id	d5uo8c_
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

Domain ID domain_id	d5uo8d_
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 (12 domains)

Domain ID domain_id	5uo8A01
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	5uo8A02
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	5uo8A03
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

Domain ID domain_id	5uo8B01
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	5uo8B02
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	5uo8B03
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

Domain ID domain_id	5uo8C01
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	5uo8C02
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	5uo8C03
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

Domain ID domain_id	5uo8D01
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	5uo8D02
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	5uo8D03
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

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Unit-cell length a length_a	59.370 Å
Unit-cell length b length_b	152.740 Å
Unit-cell length c length_c	108.511 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.74 °
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	2.180 Å
Low-resolution limit resolution_low	49.535 Å
R factor r_factor	0.2096
R_work r_work	0.2062
R_free r_free	0.2721

Structure of human endothelial nitric oxide synthase heme domain in complex with 3-[(2-aminoquinolin-7-yl)methoxy]-5-((methylamino)methyl)benzonitrile

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

Nitric oxide synthase, endothelial

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

5uo8__assembly_1__model_1

5uo8__assembly_1__model_1 | I(q)

5uo8__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 (9)

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structure of human endothelial nitric oxide synthase heme domain in complex with 3-[(2-aminoquinolin-7-yl)methoxy]-5-((methylamino)methyl)benzonitrile

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

Nitric oxide synthase, endothelial

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

5uo8__assembly_1__model_1

5uo8__assembly_1__model_1 | I(q)

5uo8__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 (9)

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)