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

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Basic information

Entry
Database: PDB / ID: 9mwi
TitleStructure of rat neuronal nitric oxide synthase R349A mutant heme domain bound with N-(3-(2-((3-(thiazole-5-carboximidamido)benzyl)amino)ethyl)phenyl)thiazole-5-carboximidamide
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 / Ion homeostasis / synaptic signaling by nitric oxide ...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 / Ion homeostasis / synaptic signaling by nitric oxide / negative regulation of vasoconstriction / response to nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / response to vitamin E / negative regulation of cytosolic calcium ion concentration / 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 / nitric-oxide synthase (NADPH) / sodium channel regulator activity / regulation of neurogenesis / negative regulation of serotonin uptake / 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 / negative regulation of blood pressure / regulation of sodium ion transport / behavioral response to cocaine / response to hormone / nitric oxide metabolic process / photoreceptor inner segment / nitric oxide biosynthetic process / T-tubule / cellular response to epinephrine stimulus / 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 protein localization / establishment of localization in cell / cellular response to mechanical stimulus / female pregnancy / negative regulation of insulin secretion / response to peptide hormone / sarcolemma / caveola / potassium ion transport / cellular response to growth factor stimulus / response to lead ion / response to estrogen / vasodilation / Z disc / calcium-dependent protein binding / calcium ion transport / FMN binding / NADP binding / flavin adenine dinucleotide 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / mitochondrial outer membrane / cytoskeleton / calmodulin binding / response to hypoxia / postsynaptic density / membrane raft / negative regulation of cell population proliferation / heme binding / synapse / dendrite / 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 / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.054 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: A step forward for neuronal Nitric Oxide Synthase Inhibitors against Melanoma
Authors: Awasthi, A. / Li, H. / Hardy, C.D. / Poulos, T.L. / Silverman, R.B.
History
DepositionJan 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1706
Polymers48,7261
Non-polymers1,4445
Water90150
1
A: Nitric oxide synthase, brain
hetero molecules

A: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,34012
Polymers97,4532
Non-polymers2,88810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area11850 Å2
ΔGint-151 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.574, 114.768, 164.710
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-804-

ZN

21A-945-

HOH

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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 / nNOS / Peptidyl-cysteine S-nitrosylase NOS1


Mass: 48726.410 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, 55 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-ACT / ACETATE ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-A1BTX / N-[3-({[2-(3-{[(Z)-imino(1,3-thiazol-5-yl)methyl]amino}phenyl)ethyl]amino}methyl)phenyl]-1,3-thiazole-5-carboximidamide


Mass: 461.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23N7S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 277 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: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 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: 2.05→39.31 Å / Num. obs: 29132 / % possible obs: 98.8 % / Redundancy: 6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Χ2: 0.73 / Net I/σ(I): 6.6 / Num. measured all: 175746
Reflection shellResolution: 2.05→2.1 Å / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 5.801 / Num. measured all: 13291 / Num. unique obs: 2230 / CC1/2: 0.334 / Rpim(I) all: 2.524 / Rrim(I) all: 6.343 / Χ2: 0.59 / Net I/σ(I) obs: 0.4

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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: 2.054→39.308 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 1385 5.1 %random
Rwork0.2065 ---
obs0.2098 27156 92.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.054→39.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 97 50 3529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093589
X-RAY DIFFRACTIONf_angle_d1.1684879
X-RAY DIFFRACTIONf_dihedral_angle_d18.8952086
X-RAY DIFFRACTIONf_chiral_restr0.051503
X-RAY DIFFRACTIONf_plane_restr0.006618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.054-2.12690.5655910.48911494X-RAY DIFFRACTION55
2.1269-2.21210.48141280.44182508X-RAY DIFFRACTION91
2.2121-2.31270.43291460.3712618X-RAY DIFFRACTION96
2.3127-2.43470.43631420.32672609X-RAY DIFFRACTION96
2.4347-2.58720.35631280.28242767X-RAY DIFFRACTION99
2.5872-2.78690.35551350.26872724X-RAY DIFFRACTION99
2.7869-3.06720.36881320.25272751X-RAY DIFFRACTION99
3.0672-3.51080.25971640.2182626X-RAY DIFFRACTION95
3.5108-4.42230.21371560.16592813X-RAY DIFFRACTION100
4.4223-39.3080.22931630.15392861X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -23.4683 Å / Origin y: -4.9686 Å / Origin z: 22.478 Å
111213212223313233
T0.3573 Å2-0.0337 Å2-0.0677 Å2-0.384 Å2-0.0071 Å2--0.4095 Å2
L0.8285 °2-0.1614 °20.5476 °2-1.2408 °20.0189 °2--7.7046 °2
S0.0031 Å °0.1355 Å °0.0121 Å °-0.0731 Å °-0.128 Å °-0.0714 Å °-0.614 Å °0.4162 Å °0.0642 Å °
Refinement TLS groupSelection details: (chain A and resid 299:716)

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