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- PDB-2hx3: Rat nNOS heme domain complexed with (4S)-N-{4-Amino-5-[(2-aminoet... -

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Basic information

Entry
Database: PDB / ID: 2hx3
TitleRat nNOS heme domain complexed with (4S)-N-{4-Amino-5-[(2-aminoethyl)-hydroxyamino]-pentyl}-N'-nitroguanidine
ComponentsNitric-oxide synthaseNitric oxide synthase
KeywordsOXIDOREDUCTASE / nitric oxide synthase / heme enzyme / inhibitor
Function / homology
Function and homology information


Ion homeostasis / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / negative regulation of hepatic stellate cell contraction / negative regulation of vasoconstriction / negative regulation of iron ion transmembrane transport / response to nitric oxide / azurophil granule / retrograde trans-synaptic signaling by nitric oxide / negative regulation of cytosolic calcium ion concentration ...Ion homeostasis / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / negative regulation of hepatic stellate cell contraction / negative regulation of vasoconstriction / negative regulation of iron ion transmembrane transport / response to nitric oxide / azurophil granule / retrograde trans-synaptic signaling by nitric oxide / negative regulation of cytosolic calcium ion concentration / positive regulation of sodium ion transmembrane transport / behavioral response to cocaine / postsynaptic specialization, intracellular component / cadmium ion binding / regulation of heart contraction / sodium channel regulator activity / postsynaptic density, intracellular component / peptidyl-cysteine S-nitrosylation / negative regulation of insulin secretion / response to vitamin E / negative regulation of heart contraction / regulation of sensory perception of pain / negative regulation of peptidyl-serine phosphorylation / cellular response to epinephrine stimulus / photoreceptor inner segment / response to organonitrogen compound / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / response to peptide hormone / response to nutrient levels / response to activity / nitric oxide mediated signal transduction / negative regulation of blood pressure / nitric-oxide synthase activity / arginine catabolic process / NADPH binding / NADPH-hemoprotein reductase activity / vesicle membrane / nitric oxide biosynthetic process / response to nicotine / response to hormone / secretory granule / phosphoprotein binding / positive regulation of long-term synaptic potentiation / sarcolemma / positive regulation of blood vessel diameter / response to organic cyclic compound / response to lead ion / establishment of protein localization / female pregnancy / positive regulation of neuron death / brain development / cellular response to mechanical stimulus / scaffold protein binding / FMN binding / ATPase binding / response to heat / ion channel binding / NADP binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / nuclear membrane / response to lipopolysaccharide / response to ethanol / negative regulation of neuron apoptotic process / calmodulin binding / dendritic spine / response to estrogen / response to hypoxia / postsynaptic density / aging / synapse / oxidoreductase activity / negative regulation of cell population proliferation / glutamatergic synapse / dendrite / heme binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / membrane / plasma membrane / nucleus / cytosol / cytoplasm
FAD-binding domain, ferredoxin reductase-type / Flavodoxin-like / Riboflavin synthase-like beta-barrel / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Oxidoreductase NAD-binding domain / Flavoprotein-like superfamily / Flavodoxin / PDZ domain / FAD binding domain / Nitric oxide synthase, oxygenase domain ...FAD-binding domain, ferredoxin reductase-type / Flavodoxin-like / Riboflavin synthase-like beta-barrel / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Oxidoreductase NAD-binding domain / Flavoprotein-like superfamily / Flavodoxin / PDZ domain / FAD binding domain / Nitric oxide synthase, oxygenase domain / PDZ superfamily / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / PDZ domain profile. / Flavodoxin-like domain profile. / Nitric oxide synthase, N-terminal domain superfamily / Oxidoreductase FAD/NAD(P)-binding / Nitric-oxide synthase, eukaryote / Flavodoxin/nitric oxide synthase / Nitric oxide synthase, N-terminal / PDZ domain / Flavoprotein pyridine nucleotide cytochrome reductase / Ferredoxin reductase-type FAD binding domain profile. / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding
Nitric oxide synthase, brain
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsIgarashi, J. / Li, H. / Poulos, T.L.
Citation
Journal: J.Med.Chem. / Year: 2007
Title: Structure-Based Design and Synthesis of N(omega)-Nitro-l-Arginine-Containing Peptidomimetics as Selective Inhibitors of Neuronal Nitric Oxide Synthase. Displacement of the Heme Structural Water.
Authors: Seo, J. / Igarashi, J. / Li, H. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis for dipeptide amide isoform-selective inhibition of neuronal nitric oxide synthase.
Authors: Flinspach, M. / Li, H. / Jamal, J. / Yang, W. / Huang, H. / Hah, J.M. / Gomez-Vidal, A. / Litzinger, E.A. / Silverman, R.B. / Poulos, T.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 2, 2006 / Release: Apr 24, 2007
RevisionDateData content typeGroupProviderType
1.0Apr 24, 2007Structure modelrepositoryInitial release
1.1Apr 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric-oxide synthase
B: Nitric-oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,05111
Polymers97,6252
Non-polymers2,4269
Water7,782432
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-80 kcal/mol
Surface area32810 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)51.910, 111.660, 164.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Nitric-oxide synthase / Nitric oxide synthase / NOS type I / Neuronal NOS / N-NOS / nNOS / Constitutive NOS / NC-NOS / BNOS


Mass: 48812.527 Da / Num. of mol.: 2 / Fragment: residues 297-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nos1, Bnos / Plasmid: pCWori / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH)

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Non-polymers , 6 types, 441 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Acetate
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Zinc
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Tetrahydrobiopterin
#6: Chemical ChemComp-3HX / (4S)-N-{4-AMINO-5-[(2-AMINOETHYL)(HYDROXYAMINO]-PENTYL}-N'-NITROGUANIDINE


Mass: 263.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H21N7O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 280 K / pH: 6
Details: PEG3350, MES, ammonium acetate, GSH, SDS, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 280K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9998
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2005 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 65600 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.559 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→49.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2485679.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3231 5 %RANDOM
Rwork0.217 ---
Obs0.217 65172 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.05 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.25 Å20 Å20 Å2
2--7.17 Å20 Å2
3----15.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 165 432 7255
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg1.4
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d22.4
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d1.01
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it1.491.5
c_mcangle_it2.352
c_scbond_it2.062
c_scangle_it2.942.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 504 4.7 %
Rwork0.296 10195 -
Obs--99.9 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1PROTEIN_REP.PARAMPROTEIN.TOP
2HETERO.PARHETERO.TOP
3WATER_REP.PARAMWATER_REP.TOP
43HX.PAR3HX.TOP

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