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

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Basic information

Entry
Database: PDB / ID: 9mwe
TitleStructure of rat neuronal nitric oxide synthase R349A mutant heme domain bound with N-(4-(2-((3-(furan-3-carboximidamido)benzyl)amino)ethyl)phenyl)furan-3-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 / sodium channel regulator activity / nitric-oxide synthase (NADPH) / regulation of neurogenesis / negative regulation of serotonin uptake / nitric-oxide synthase activity / xenobiotic catabolic process / multicellular organismal response to stress / L-arginine catabolic process / NADPH binding / postsynaptic density, intracellular component / striated muscle contraction / nitric oxide-cGMP-mediated signaling / negative regulation of blood pressure / regulation of sodium ion transport / response to hormone / behavioral response to cocaine / 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 protein localization / establishment of localization in cell / female pregnancy / cellular response to mechanical stimulus / negative regulation of insulin secretion / sarcolemma / response to peptide hormone / caveola / potassium ion transport / response to lead ion / cellular response to growth factor stimulus / 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 / response to hypoxia / mitochondrial outer membrane / cytoskeleton / calmodulin binding / 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 / Xylitol / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.04 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

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2887
Polymers48,7261
Non-polymers1,5626
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.039, 114.473, 164.584
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

21A-940-

HOH

31A-942-

HOH

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Components

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Protein / Sugars , 2 types, 2 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)
#7: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O5

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Non-polymers , 6 types, 62 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-A1BT3 / N-[3-({[2-(4-{[(E)-(furan-3-yl)(imino)methyl]amino}phenyl)ethyl]amino}methyl)phenyl]furan-3-carboximidamide


Mass: 427.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25N5O2 / 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2024 / 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: 2.04→46.99 Å / Num. obs: 30055 / % possible obs: 100 % / Redundancy: 18.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.059 / Rrim(I) all: 0.25 / Net I/σ(I): 7.4 / Num. measured all: 551540
Reflection shellResolution: 2.04→2.1 Å / % possible obs: 99.8 % / Redundancy: 16.8 % / Rmerge(I) obs: 6.363 / Num. measured all: 38258 / Num. unique obs: 2280 / CC1/2: 0.594 / Rpim(I) all: 1.602 / Rrim(I) all: 6.565 / Net I/σ(I) obs: 0.6

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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: 2.04→45.077 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 39.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 2781 5.01 %random
Rwork0.2071 ---
obs0.21 29335 97.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→45.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 107 57 3485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063536
X-RAY DIFFRACTIONf_angle_d0.9614809
X-RAY DIFFRACTIONf_dihedral_angle_d19.022051
X-RAY DIFFRACTIONf_chiral_restr0.049499
X-RAY DIFFRACTIONf_plane_restr0.005607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0401-2.07520.4349890.37772398X-RAY DIFFRACTION86
2.0752-2.1130.43751240.36792296X-RAY DIFFRACTION87
2.113-2.15360.42111440.33722493X-RAY DIFFRACTION91
2.1536-2.19760.36831350.33162539X-RAY DIFFRACTION95
2.1976-2.24540.41791360.31792637X-RAY DIFFRACTION97
2.2454-2.29760.36221590.30272673X-RAY DIFFRACTION99
2.2976-2.3550.4281260.2892643X-RAY DIFFRACTION98
2.355-2.41870.39351570.28692693X-RAY DIFFRACTION99
2.4187-2.48990.35831240.27862730X-RAY DIFFRACTION99
2.4899-2.57020.37161260.26342684X-RAY DIFFRACTION99
2.5702-2.66210.33971430.26322663X-RAY DIFFRACTION99
2.6621-2.76870.3261220.26382667X-RAY DIFFRACTION99
2.7687-2.89470.33191390.24422722X-RAY DIFFRACTION99
2.8947-3.04720.33621210.24842707X-RAY DIFFRACTION99
3.0472-3.23810.2691540.22592704X-RAY DIFFRACTION100
3.2381-3.4880.2431740.21222686X-RAY DIFFRACTION100
3.488-3.83890.23031460.17852670X-RAY DIFFRACTION100
3.8389-4.3940.20521540.16122718X-RAY DIFFRACTION100
4.394-5.53440.22391660.14842669X-RAY DIFFRACTION100
5.5344-45.0770.20141420.16022705X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -23.5826 Å / Origin y: -4.8766 Å / Origin z: 22.2999 Å
111213212223313233
T0.2591 Å2-0.0093 Å2-0.0269 Å2-0.364 Å2-0.0092 Å2--0.4589 Å2
L0.943 °2-0.1973 °2-0.3734 °2-1.2807 °20.6891 °2--9.8151 °2
S-0.0699 Å °0.1563 Å °-0.0453 Å °0.0121 Å °-0.1468 Å °0.0069 Å °-0.0957 Å °0.054 Å °0.1461 Å °
Refinement TLS groupSelection details: (chain A and resid 302:716)

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