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- PDB-7s3y: Structure ofrat neuronal nitric oxide synthase heme domain in com... -

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Basic information

Entry
Database: PDB / ID: 7s3y
TitleStructure ofrat neuronal nitric oxide synthase heme domain in complex with 7-((3-(2-(6-aminopyridin-2-yl)ethyl)phenoxy)methyl)quinolin-2-amine
ComponentsNitric oxide synthase, brain
KeywordsOXIDOREDUCTASE/Inhibitor / nitric oxide synthase inhibitor / heme enzyme / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / ROS and RNS production in phagocytes / postsynaptic specialization, intracellular component / peptidyl-cysteine S-nitrosylation / Ion homeostasis / negative regulation of vasoconstriction ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / ROS and RNS production in phagocytes / postsynaptic specialization, intracellular component / peptidyl-cysteine S-nitrosylation / Ion homeostasis / negative regulation of vasoconstriction / synaptic signaling by nitric oxide / azurophil granule / response to nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of hydrolase activity / positive regulation of sodium ion transmembrane transport / peptidyl-cysteine S-nitrosylase activity / response to vitamin E / negative regulation of calcium ion transport / negative regulation of potassium ion transport / regulation of sodium ion transport / positive regulation of the force of heart contraction / cadmium ion binding / neuron projection terminus / negative regulation of cytosolic calcium ion concentration / sodium channel regulator activity / nitric-oxide synthase (NADPH) / regulation of postsynaptic membrane potential / multicellular organismal response to stress / negative regulation of insulin secretion / regulation of neurogenesis / nitric-oxide synthase activity / xenobiotic catabolic process / negative regulation of serotonin uptake / NADPH binding / L-arginine catabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of blood pressure / postsynaptic density, intracellular component / nitric oxide metabolic process / nitric oxide biosynthetic process / behavioral response to cocaine / response to hormone / photoreceptor inner segment / cellular response to epinephrine stimulus / sarcoplasmic reticulum membrane / T-tubule / secretory granule / response to activity / calyx of Held / positive regulation of long-term synaptic potentiation / cell periphery / response to nicotine / sarcoplasmic reticulum / striated muscle contraction / female pregnancy / establishment of protein localization / phosphoprotein binding / vasodilation / response to nutrient levels / sarcolemma / response to estrogen / caveola / response to lead ion / cellular response to growth factor stimulus / response to peptide hormone / cellular response to mechanical stimulus / Z disc / positive regulation of neuron apoptotic process / calcium-dependent protein binding / NADP binding / FMN binding / flavin adenine dinucleotide binding / negative regulation of neuron apoptotic process / response to heat / nuclear membrane / ATPase binding / response to lipopolysaccharide / scaffold protein binding / calmodulin binding / response to hypoxia / cytoskeleton / dendritic spine / RNA polymerase II-specific DNA-binding transcription factor binding / response to ethanol / perikaryon / transmembrane transporter binding / mitochondrial outer membrane / postsynaptic density / membrane raft / negative regulation of cell population proliferation / heme binding / negative regulation of apoptotic process / dendrite / positive regulation of DNA-templated transcription / synapse / glutamatergic synapse / perinuclear region of cytoplasm / 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-V5G / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 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)GM57353 United States
CitationJournal: To be published
Title: Selective anti-MRSA inhibitors targeting bacterial nitric oxide synthase
Authors: Lewis, M.C. / Weerawarna, P.M. / Li, H. / Murarka, V. / Silverman, R.B. / Poulos, T.L.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase, brain
B: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,44913
Polymers97,6252
Non-polymers2,82411
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-87 kcal/mol
Surface area32320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.430, 110.381, 163.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 48812.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nos1, Bnos / Organ: brain / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29476, nitric-oxide synthase (NADPH)

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Non-polymers , 7 types, 299 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Chemical ChemComp-V5G / 7-({3-[2-(6-aminopyridin-2-yl)ethyl]phenoxy}methyl)quinolin-2-amine


Mass: 370.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: 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.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: brick
Crystal growTemperature: 277 K / Method: vapor diffusion / 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: Dec 3, 2017 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→65.72 Å / Num. obs: 105537 / % possible obs: 98.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 35.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.07 / Rrim(I) all: 0.166 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.08-2.145.62.9362388342480.4321.3323.2310.797.7
9.07-65.7250.03239147770.9990.0160.03628.197.5

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1-2575_1496refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.08→48.887 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 31.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 5238 4.97 %random
Rwork0.1898 100205 --
obs0.192 105443 97.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.68 Å2 / Biso mean: 55.7971 Å2 / Biso min: 21.72 Å2
Refinement stepCycle: final / Resolution: 2.08→48.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 197 288 7144
Biso mean--47.49 49.88 -
Num. residues----818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077095
X-RAY DIFFRACTIONf_angle_d0.9669652
X-RAY DIFFRACTIONf_chiral_restr0.049994
X-RAY DIFFRACTIONf_plane_restr0.0051217
X-RAY DIFFRACTIONf_dihedral_angle_d17.5024126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.08-2.10360.42181350.376335497
2.1036-2.12840.40861450.3549331897
2.1284-2.15440.37791540.3517333497
2.1544-2.18160.42121610.3487327797
2.1816-2.21030.36371790.3298333697
2.2103-2.24060.40731830.3212333197
2.2406-2.27260.37552230.3108322597
2.2726-2.30650.35531770.3016331597
2.3065-2.34260.33281850.2861341497
2.3426-2.3810.35341660.2707326497
2.381-2.4220.32831620.2712331897
2.422-2.46610.34741710.2844336798
2.4661-2.51350.37381690.2594332597
2.5135-2.56480.32161920.2541336798
2.5648-2.62060.28121560.2483331998
2.6206-2.68150.29311730.2412336598
2.6815-2.74860.27561540.2318335698
2.7486-2.82290.24261770.2065336698
2.8229-2.9060.27451800.2097336098
2.906-2.99970.21931770.2035334498
2.9997-3.10690.25312000.2041328898
3.1069-3.23130.23871680.1879341198
3.2313-3.37830.20421800.1689332698
3.3783-3.55640.18711570.1587336598
3.5564-3.77910.21562040.1487333498
3.7791-4.07080.21351630.1284338098
4.0708-4.48020.13461830.1182333798
4.4802-5.12790.17642160.1179335998
5.1279-6.45830.18511960.141335899
6.4583-48.8870.15861520.1544339298
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)
11.0548-0.2618-0.2731.26230.07286.73-0.0260.1136-0.00840.0584-0.06970.052-0.0159-0.24790.05950.2885-0.00440.00120.2461-0.0050.254611.21644.714622.576
20.9928-0.2984-0.14651.2240.39753.22370.0074-0.0220.0512-0.11-0.0718-0.01850.10030.13760.05490.22040.00350.03360.23270.01690.240112.32394.840959.7219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 299:716)A299 - 716
2X-RAY DIFFRACTION2(chain B and resid 299:718)B299 - 718

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