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- PDB-9q4v: Structure of rat neuronal nitric oxide synthase R349A mutant heme... -

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Basic information

Entry
Database: PDB / ID: 9q4v
TitleStructure of rat neuronal nitric oxide synthase R349A mutant heme domain bound with 6-((2,3-difluoro-5-(2-(4-fluoropiperidin-1-yl)ethyl)phenoxy)methyl)-4-methylpyridin-2-amine
ComponentsNitric oxide synthase, brain
KeywordsOXIDOREDUCTASE/INHIBITOR / nitric oxide synthase inhibitor binding / OXIDOREDUCTASE-INHIBITOR complex / OXIDOREDUCTASE
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 / NADPH binding / postsynaptic density, intracellular component / striated muscle contraction / nitric oxide-cGMP-mediated signaling / behavioral response to cocaine / regulation of sodium ion transport / 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 / phosphoprotein binding / response to nutrient levels / establishment of localization in cell / establishment of protein localization / negative regulation of insulin secretion / cellular response to mechanical stimulus / female pregnancy / 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
: / 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: 2.14 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0295
Polymers48,7261
Non-polymers1,3034
Water41423
1
A: Nitric oxide synthase, brain
hetero molecules

A: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,05810
Polymers97,4532
Non-polymers2,6058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3_455-x-1,y,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)49.013, 114.137, 164.281
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-803-

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 / 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 , 5 types, 27 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-A1COK / 6-[(2,3-difluoro-5-{2-[(3S)-3-fluoropiperidin-1-yl]ethyl}phenoxy)methyl]-4-methylpyridin-2-amine


Mass: 379.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24F3N3O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2023 / 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: 2.14→46.87 Å / Num. obs: 25861 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.096 / Rrim(I) all: 0.226 / Χ2: 1.05 / Net I/σ(I): 5.3 / Num. measured all: 140306
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 9.999 / Num. unique obs: 2079 / CC1/2: 0.355 / Rpim(I) all: 5.47 / Rrim(I) all: 13.343 / Χ2: 1.02

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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: 2.14→46.867 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 45.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2842 2245 5.06 %random
Rwork0.2234 ---
obs0.2266 23728 90.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→46.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 88 23 3489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083580
X-RAY DIFFRACTIONf_angle_d1.1214872
X-RAY DIFFRACTIONf_dihedral_angle_d19.0682091
X-RAY DIFFRACTIONf_chiral_restr0.051506
X-RAY DIFFRACTIONf_plane_restr0.006614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.18650.45111130.3842028X-RAY DIFFRACTION71
2.1865-2.23740.45521060.38992180X-RAY DIFFRACTION74
2.2374-2.29340.44881320.40962165X-RAY DIFFRACTION75
2.2934-2.35540.46171000.35692302X-RAY DIFFRACTION79
2.3554-2.42470.44851380.35192406X-RAY DIFFRACTION82
2.4247-2.50290.43221220.32172538X-RAY DIFFRACTION87
2.5029-2.59240.36881290.31332658X-RAY DIFFRACTION89
2.5924-2.69620.40271380.3392751X-RAY DIFFRACTION95
2.6962-2.81890.40091360.32732865X-RAY DIFFRACTION98
2.8189-2.96740.45761250.31542881X-RAY DIFFRACTION99
2.9674-3.15330.35141600.29192871X-RAY DIFFRACTION99
3.1533-3.39670.32321840.26462863X-RAY DIFFRACTION100
3.3967-3.73840.27011700.22822907X-RAY DIFFRACTION99
3.7384-4.27910.24781670.18052893X-RAY DIFFRACTION100
4.2791-5.38990.24691640.15392901X-RAY DIFFRACTION100
5.3899-46.8670.17441610.1462900X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -23.6152 Å / Origin y: -5.1066 Å / Origin z: 22.4098 Å
111213212223313233
T0.2659 Å2-0.0095 Å2-0.0873 Å2-0.3568 Å2-0.0149 Å2--0.4077 Å2
L1.0941 °2-0.1574 °20.1524 °2-1.5207 °2-0.0711 °2--9.3297 °2
S-0.0615 Å °0.1403 Å °-0.0206 Å °-0.0187 Å °-0.0702 Å °-0.0833 Å °-0.3159 Å °0.3616 Å °0.0973 Å °
Refinement TLS groupSelection details: (chain A and resid 299:716)

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