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- PDB-9cvi: Structure of rat neuronal nitric oxide synthase R349A mutant heme... -

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Basic information

Entry
Database: PDB / ID: 9cvi
TitleStructure of rat neuronal nitric oxide synthase R349A mutant heme domain bound with 4-methyl-6-(3-((methylamino)methyl)phenyl)pyridin-2-amine dihydrochloride
ComponentsNitric oxide synthase, brain
KeywordsOXIDOREDUCTASE / nitric oxide synthase inhibitor binding
Function / homology
Function and homology information


negative regulation of hepatic stellate cell contraction / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / postsynaptic specialization, intracellular component / ROS and RNS production in phagocytes / azurophil granule / synaptic signaling by nitric oxide / Ion homeostasis ...negative regulation of hepatic stellate cell contraction / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / postsynaptic specialization, intracellular component / ROS and RNS production in phagocytes / azurophil granule / synaptic signaling by nitric oxide / Ion homeostasis / negative regulation of vasoconstriction / response to nitric oxide / negative regulation of cytosolic calcium ion concentration / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / response to vitamin E / 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 / nitric-oxide synthase (NADPH) / sodium channel regulator activity / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / L-arginine catabolic process / postsynaptic density, intracellular component / NADPH binding / striated muscle contraction / nitric oxide-cGMP-mediated signaling / regulation of sodium ion transport / behavioral response to cocaine / negative regulation of blood pressure / response to hormone / nitric oxide metabolic process / nitric oxide biosynthetic process / photoreceptor inner segment / cellular response to epinephrine stimulus / T-tubule / sarcoplasmic reticulum membrane / secretory granule / calyx of Held / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / response to activity / cell periphery / response to nicotine / response to nutrient levels / phosphoprotein binding / establishment of localization in cell / establishment of protein localization / female pregnancy / cellular response to mechanical stimulus / negative regulation of insulin secretion / response to peptide hormone / sarcolemma / caveola / cellular response to growth factor stimulus / potassium ion transport / response to lead ion / response to estrogen / vasodilation / Z disc / calcium-dependent protein binding / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / NADP binding / positive regulation of neuron apoptotic process / ATPase binding / response to heat / scaffold protein binding / response to ethanol / nuclear membrane / response to lipopolysaccharide / dendritic spine / negative regulation of neuron apoptotic process / transmembrane transporter binding / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / cytoskeleton / calmodulin binding / response to hypoxia / postsynaptic density / membrane raft / negative regulation of cell population proliferation / heme binding / dendrite / synapse / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II
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
ACETATE ION / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-KMI / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 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: Bioorg.Med.Chem. / Year: 2025
Title: Truncated pyridinylbenzylamines: Potent, selective, and highly membrane permeable inhibitors of human neuronal nitric oxide synthase.
Authors: Vasu, D. / Do, H.T. / Li, H. / Hardy, C.D. / Poulos, T.L. / Silverman, R.B.
History
DepositionJul 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9456
Polymers48,7351
Non-polymers1,2095
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.545, 114.161, 163.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-805-

ZN

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 48735.438 Da / Num. of mol.: 1 / Mutation: R349A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nos1, Bnos / Organ: brain / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29476, nitric-oxide synthase (NADPH)

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Non-polymers , 6 types, 35 molecules

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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Chemical ChemComp-KMI / 4-methyl-6-{3-[(methylamino)methyl]phenyl}pyridin-2-amine


Mass: 227.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: bricks
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 20-24% PEG3350, 0.1M MES 0.14-0.20M AMMONIUM ACETATE, 10% ETHYLENE GLYCOL, 30uM SDS, 5 mM GSH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2021 / 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: 2.03→46.84 Å / Num. obs: 29446 / % possible obs: 98.4 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.068 / Rrim(I) all: 0.157 / Χ2: 1.04 / Net I/σ(I): 5.9 / Num. measured all: 163416
Reflection shellResolution: 2.03→2.08 Å / % possible obs: 98.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 4.729 / Num. measured all: 12502 / Num. unique obs: 2158 / CC1/2: 0.344 / Rpim(I) all: 2.128 / Rrim(I) all: 5.194 / Χ2: 1.02 / Net I/σ(I) obs: 0.5

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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: 2.03→46.84 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 44.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2973 2599 5.01 %random
Rwork0.2338 ---
obs0.2371 27504 91.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 82 30 3445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083526
X-RAY DIFFRACTIONf_angle_d1.0814798
X-RAY DIFFRACTIONf_dihedral_angle_d18.8822052
X-RAY DIFFRACTIONf_chiral_restr0.05498
X-RAY DIFFRACTIONf_plane_restr0.006606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.06690.4756870.45262242X-RAY DIFFRACTION77
2.0669-2.10670.47281210.42442171X-RAY DIFFRACTION77
2.1067-2.14970.38341200.39692313X-RAY DIFFRACTION81
2.1497-2.19640.41081200.37362315X-RAY DIFFRACTION81
2.1964-2.24750.44371400.36942373X-RAY DIFFRACTION84
2.2475-2.30370.39321400.34372447X-RAY DIFFRACTION85
2.3037-2.3660.39021200.33032473X-RAY DIFFRACTION89
2.366-2.43570.40511350.33442621X-RAY DIFFRACTION91
2.4357-2.51430.4221320.32792696X-RAY DIFFRACTION96
2.5143-2.60410.34091290.32752775X-RAY DIFFRACTION97
2.6041-2.70840.39511490.32092815X-RAY DIFFRACTION98
2.7084-2.83160.35271420.29462786X-RAY DIFFRACTION98
2.8316-2.98090.40491090.28662830X-RAY DIFFRACTION98
2.9809-3.16760.32371690.28132758X-RAY DIFFRACTION98
3.1676-3.41210.30331760.28392764X-RAY DIFFRACTION98
3.4121-3.75540.29231570.24182741X-RAY DIFFRACTION97
3.7554-4.29840.27681540.20792684X-RAY DIFFRACTION95
4.2984-5.41430.27061510.16682695X-RAY DIFFRACTION94
5.4143-46.840.21711480.15332747X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -23.4533 Å / Origin y: -4.9805 Å / Origin z: 22.2786 Å
111213212223313233
T0.2594 Å2-0.0178 Å2-0.0469 Å2-0.4272 Å2-0.0104 Å2--0.4573 Å2
L0.7491 °2-0.185 °20.271 °2-1.0566 °2-0.0602 °2--7.6263 °2
S0.0117 Å °0.1294 Å °-0.0194 Å °0.0988 Å °-0.0726 Å °-0.0256 Å °-0.1122 Å °0.3041 Å °0.0557 Å °
Refinement TLS groupSelection details: (chain A and resid 299:716)

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