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- PDB-9myw: Structure of human neuronal nitric oxide synthase R354A/G357D mut... -

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Basic information

Entry
Database: PDB / ID: 9myw
TitleStructure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain bound 2-(2-amino-6-fluoro-4-methylquinolin-7-yl)-5-(2-aminoethyl)phenol
ComponentsNitric oxide synthase, brain
KeywordsOXIDOREDUCTASE / nitric oxide synthase inhibitor binding / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of calcium ion transport into cytosol / Nitric oxide stimulates guanylate cyclase / myoblast fusion / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / regulation of cardiac muscle contraction by calcium ion signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / synaptic signaling by nitric oxide ...positive regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of calcium ion transport into cytosol / Nitric oxide stimulates guanylate cyclase / myoblast fusion / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / regulation of cardiac muscle contraction by calcium ion signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / synaptic signaling by nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of sodium ion transmembrane transport / peptidyl-cysteine S-nitrosylase activity / positive regulation of the force of heart contraction / cadmium ion binding / negative regulation of calcium ion transport / negative regulation of potassium ion transport / regulation of postsynaptic membrane potential / nitric oxide mediated signal transduction / sodium channel regulator activity / nitric-oxide synthase (NADPH) / regulation of neurogenesis / regulation of cardiac muscle contraction / negative regulation of serotonin uptake / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / L-arginine catabolic process / striated muscle contraction / negative regulation of blood pressure / regulation of sodium ion transport / Ion homeostasis / response to hormone / photoreceptor inner segment / nitric oxide biosynthetic process / T-tubule / sarcoplasmic reticulum membrane / cell redox homeostasis / calyx of Held / sarcoplasmic reticulum / cell periphery / calcium channel regulator activity / establishment of localization in cell / sarcolemma / caveola / potassium ion transport / cellular response to growth factor stimulus / vasodilation / Z disc / calcium-dependent protein binding / calcium ion transport / FMN binding / NADP binding / flavin adenine dinucleotide binding / positive regulation of neuron apoptotic process / response to heat / scaffold protein binding / response to lipopolysaccharide / dendritic spine / transmembrane transporter binding / calmodulin binding / response to hypoxia / cytoskeleton / postsynaptic density / membrane raft / heme binding / synapse / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding ...Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / PDZ domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
: / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.305 Å
AuthorsLi, H. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131920 United States
CitationJournal: To Be Published
Title: Design and synthesis of 7-aryl-6-fluoro-2-aminoquinolines as potent and highly selective human neuronal nitric oxide synthase inhibitors
Authors: Ansari, A. / Rathnayake, A.D. / Li, H. / Hardy, C.D. / Poulos, T.L. / Silverman, R.B.
History
DepositionJan 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitric oxide synthase, brain
B: Nitric oxide synthase, brain
C: Nitric oxide synthase, brain
D: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,34724
Polymers195,9874
Non-polymers5,36020
Water10,665592
1
A: Nitric oxide synthase, brain
B: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,67312
Polymers97,9942
Non-polymers2,68010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-122 kcal/mol
Surface area34330 Å2
MethodPISA
2
C: Nitric oxide synthase, brain
D: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,67312
Polymers97,9942
Non-polymers2,68010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-123 kcal/mol
Surface area34290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.280, 118.366, 164.846
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Nitric oxide synthase, brain / Constitutive NOS / NC-NOS / NOS type I / Neuronal NOS / nNOS / Peptidyl-cysteine S-nitrosylase NOS1 / bNOS


Mass: 48996.781 Da / Num. of mol.: 4 / Mutation: R354A, G357D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOS1 / Organ: brain / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE30 / References: UniProt: P29475, nitric-oxide synthase (NADPH)

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Non-polymers , 6 types, 612 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Chemical
ChemComp-A1BUH / (2M)-5-(2-aminoethyl)-2-(2-amino-6-fluoro-4-methylquinolin-7-yl)phenol


Mass: 311.353 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18FN3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.2 % / Description: plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 8% PEG3350 35mM citric acid 65mM Bis-Tris-Propane 10% glycerol 5mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2024 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→39.46 Å / Num. obs: 87948 / % possible obs: 98.8 % / Redundancy: 3.2 % / CC1/2: 0.971 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.073 / Rrim(I) all: 0.135 / Χ2: 0.86 / Net I/σ(I): 6.1 / Num. measured all: 278016
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 1.559 / Num. unique obs: 4419 / CC1/2: 0.72 / Rpim(I) all: 1.07 / Rrim(I) all: 1.9 / Χ2: 1.52 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.305→39.182 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.85 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 7787 4.94 %random
Rwork0.1814 ---
obs0.1847 86572 90.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.305→39.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13558 0 370 592 14520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714425
X-RAY DIFFRACTIONf_angle_d0.93819650
X-RAY DIFFRACTIONf_dihedral_angle_d17.8728414
X-RAY DIFFRACTIONf_chiral_restr0.0522028
X-RAY DIFFRACTIONf_plane_restr0.0052480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3052-2.33140.47422140.39444138X-RAY DIFFRACTION74
2.3314-2.35890.42412350.36194453X-RAY DIFFRACTION81
2.3589-2.38760.31892030.29244925X-RAY DIFFRACTION88
2.3876-2.41780.34792530.29084888X-RAY DIFFRACTION89
2.4178-2.44970.36162790.28294926X-RAY DIFFRACTION89
2.4497-2.48320.32392410.28544908X-RAY DIFFRACTION88
2.4832-2.51870.3172360.27174695X-RAY DIFFRACTION86
2.5187-2.55630.34482330.25054963X-RAY DIFFRACTION89
2.5563-2.59620.28092390.22355136X-RAY DIFFRACTION91
2.5962-2.63880.25872690.23984988X-RAY DIFFRACTION91
2.6388-2.68430.31972540.24984995X-RAY DIFFRACTION91
2.6843-2.73310.32672640.25755115X-RAY DIFFRACTION92
2.7331-2.78560.36192810.23835070X-RAY DIFFRACTION92
2.7856-2.84240.25592900.2164956X-RAY DIFFRACTION91
2.8424-2.90420.29932820.21365135X-RAY DIFFRACTION92
2.9042-2.97180.3032660.20794947X-RAY DIFFRACTION91
2.9718-3.04610.27862460.21445126X-RAY DIFFRACTION92
3.0461-3.12840.2742740.21455068X-RAY DIFFRACTION92
3.1284-3.22040.30112830.21285087X-RAY DIFFRACTION92
3.2204-3.32430.25972640.19155056X-RAY DIFFRACTION92
3.3243-3.4430.27292230.17245076X-RAY DIFFRACTION92
3.443-3.58080.21862800.16365012X-RAY DIFFRACTION91
3.5808-3.74370.25682580.15274976X-RAY DIFFRACTION89
3.7437-3.94080.22242560.15575139X-RAY DIFFRACTION93
3.9408-4.18750.19412690.12885162X-RAY DIFFRACTION94
4.1875-4.51040.19262930.12695204X-RAY DIFFRACTION94
4.5104-4.96350.18183100.12315189X-RAY DIFFRACTION94
4.9635-5.67980.20912860.13835206X-RAY DIFFRACTION94
5.6798-7.14890.19652480.14945142X-RAY DIFFRACTION93
7.1489-39.1820.192580.15985281X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4235-0.2081-0.14330.6221-0.21282.10810.00990.040.03220.0783-0.0549-0.0903-0.12790.07760.03310.2478-0.0115-0.03650.3088-0.00190.2848-10.8715-4.5757-40.1612
20.3956-0.1721-0.17830.73670.02951.37170.0027-0.0093-0.0673-0.0423-0.01230.0383-0.0222-0.03890.01670.2326-0.004-0.04140.2972-0.02570.3069-12.9262-4.3284-2.5735
30.35970.17450.15410.72680.01581.35930.0305-0.01340.06470.0635-0.02920.0596-0.0199-0.0641-0.01080.24040.00510.04560.2906-0.01440.311913.3108-54.159-79.8354
40.46710.24210.08430.5966-0.06532.12820.0123-0.0479-0.0254-0.0322-0.0466-0.06460.1060.08910.02490.27060.00240.03850.313-0.00220.292615.2591-53.8574-42.2669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 305:722)
2X-RAY DIFFRACTION2(chain B and resid 305:722)
3X-RAY DIFFRACTION3(chain C and resid 305:722)
4X-RAY DIFFRACTION4(chain D and resid 305:722)

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