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- PDB-9q4g: Structure of human neuronal nitric oxide synthase R354A/G357D mut... -

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Basic information

Entry
Database: PDB / ID: 9q4g
TitleStructure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain bound 6-((5-(2-(dimethylamino)ethyl)-2,3-difluorophenoxy)methyl)-4-methylpyridin-2-amine
ComponentsNitric oxide synthase, brain
KeywordsOXIDOREDUCTASE/INHIBITOR / 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 / cadmium ion binding / positive regulation of the force of heart contraction / 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) / negative regulation of serotonin uptake / regulation of neurogenesis / regulation of cardiac muscle contraction / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / L-arginine catabolic process / striated muscle contraction / regulation of sodium ion transport / Ion homeostasis / negative regulation of blood pressure / response to hormone / nitric oxide biosynthetic process / photoreceptor inner segment / 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 / cellular response to growth factor stimulus / potassium ion transport / vasodilation / Z disc / calcium-dependent protein binding / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / NADP binding / positive regulation of neuron apoptotic process / response to heat / scaffold protein binding / response to lipopolysaccharide / dendritic spine / transmembrane transporter binding / cytoskeleton / calmodulin binding / response to hypoxia / 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: 2.3 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: Highly potent, selective, and membrane permeable ether linked 2-aminopyridine-based human neuronal nitric oxide synthase inhibitors
Authors: Ansari, A. / Chrzanowski, R.T. / Li, H. / Hardy, C.D. / Poulos, T.L. / Silverman, R.B.
History
DepositionAug 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 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)201,38724
Polymers195,9874
Non-polymers5,40020
Water9,656536
1
A: Nitric oxide synthase, brain
B: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,69312
Polymers97,9942
Non-polymers2,70010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-85 kcal/mol
Surface area33850 Å2
MethodPISA
2
C: Nitric oxide synthase, brain
D: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,69312
Polymers97,9942
Non-polymers2,70010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-85 kcal/mol
Surface area34120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.193, 118.348, 164.637
Angle α, β, γ (deg.)90.00, 90.04, 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) / References: UniProt: P29475, nitric-oxide synthase (NADPH)

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Non-polymers , 6 types, 556 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-A1CN2 / 6-({5-[2-(dimethylamino)ethyl]-2,3-difluorophenoxy}methyl)-4-methylpyridin-2-amine


Mass: 321.365 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21F2N3O / 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.: 536 / 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, 35 mM citric acid, 65 mM Bis-Tris-propane, 10% glycerol, 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2022 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.05 Å / Num. obs: 88693 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.918 / Rmerge(I) obs: 0.429 / Rpim(I) all: 0.217 / Rrim(I) all: 0.483 / Net I/σ(I): 3.9 / Num. measured all: 423150
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.4 % / Rmerge(I) obs: 4.629 / Num. unique obs: 4491 / CC1/2: 0.087 / Rpim(I) all: 2.408 / Rrim(I) all: 5.24 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→48.048 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 34.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.298 8714 4.99 %random
Rwork0.2219 ---
obs0.2256 88589 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13558 0 370 536 14464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914414
X-RAY DIFFRACTIONf_angle_d1.05119624
X-RAY DIFFRACTIONf_dihedral_angle_d18.0718418
X-RAY DIFFRACTIONf_chiral_restr0.0542028
X-RAY DIFFRACTIONf_plane_restr0.0072479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.40373170.31985569X-RAY DIFFRACTION99
2.3261-2.35350.37383010.31225529X-RAY DIFFRACTION100
2.3535-2.38220.43113060.30395496X-RAY DIFFRACTION100
2.3822-2.41240.35932720.31285418X-RAY DIFFRACTION99
2.4124-2.44410.41262770.31245522X-RAY DIFFRACTION99
2.4441-2.47760.37263060.32395491X-RAY DIFFRACTION100
2.4776-2.5130.3783210.30975493X-RAY DIFFRACTION100
2.513-2.55050.38212640.30995567X-RAY DIFFRACTION100
2.5505-2.59030.38623170.30575569X-RAY DIFFRACTION100
2.5903-2.63280.38192860.30395529X-RAY DIFFRACTION100
2.6328-2.67820.44513190.37355376X-RAY DIFFRACTION98
2.6782-2.72690.41862760.32955572X-RAY DIFFRACTION100
2.7269-2.77930.34732760.3025608X-RAY DIFFRACTION100
2.7793-2.83610.3972900.29325448X-RAY DIFFRACTION100
2.8361-2.89770.32512780.27185698X-RAY DIFFRACTION100
2.8977-2.96510.32632540.27915460X-RAY DIFFRACTION100
2.9651-3.03930.34782880.26085629X-RAY DIFFRACTION100
3.0393-3.12140.3562730.25625556X-RAY DIFFRACTION100
3.1214-3.21320.31122660.25185560X-RAY DIFFRACTION100
3.2132-3.31690.34622930.23445509X-RAY DIFFRACTION100
3.3169-3.43550.33023310.24745499X-RAY DIFFRACTION100
3.4355-3.5730.32513050.2355470X-RAY DIFFRACTION99
3.573-3.73550.29032930.19595569X-RAY DIFFRACTION100
3.7355-3.93240.26593100.19755493X-RAY DIFFRACTION100
3.9324-4.17860.22712960.15385485X-RAY DIFFRACTION100
4.1786-4.5010.18693000.13925519X-RAY DIFFRACTION100
4.501-4.95360.20472560.12925605X-RAY DIFFRACTION100
4.9536-5.66940.23243140.14925519X-RAY DIFFRACTION100
5.6694-7.13910.21642720.1595561X-RAY DIFFRACTION100
7.1391-48.0480.21942570.1595541X-RAY DIFFRACTION99
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)
10.2935-0.18-0.00190.5032-0.10692.17440.05360.0402-0.01660.0324-0.0514-0.0406-0.06750.11450.01020.2724-0.0109-0.02580.2529-0.00490.2658-10.7584-4.6384-40.1106
20.4759-0.1583-0.25840.4256-0.01541.34130.00590.0123-0.0783-0.0405-0.0310.048-0.02-0.0390.01990.2513-0.0012-0.04750.2792-0.02050.3262-12.9074-4.4792-2.5196
30.5370.17790.29830.65910.06911.37540.00950.00910.09660.0623-0.03730.03560.0317-0.06130.0220.20740.01460.05560.2256-0.02130.257913.1799-54.0422-79.8263
40.30670.0303-0.05860.5771-0.11212.11850.041-0.0238-0.0131-0.0733-0.0582-0.08520.06140.07910.0210.27780.00170.02970.28180.00830.292515.3196-53.7496-42.2219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 302:722)
2X-RAY DIFFRACTION2(chain B and resid 304:722)
3X-RAY DIFFRACTION3(chain C and resid 302:722)
4X-RAY DIFFRACTION4(chain D and resid 304:724)

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