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- PDB-4v3x: Structure of rat neuronal nitric oxide synthase heme domain in co... -

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Basic information

Entry
Database: PDB / ID: 4v3x
TitleStructure of rat neuronal nitric oxide synthase heme domain in complex with N-2-(2-(1H-imidazol-1-yl)pyrimidin-4-yl)ethyl-3-(3- fluorophenyl)propan-1-amine
ComponentsNITRIC OXIDE SYNTHASE, BRAIN
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


synaptic signaling by nitric oxide / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of hepatic stellate cell contraction / ROS and RNS production in phagocytes / negative regulation of iron ion transmembrane transport / negative regulation of vasoconstriction / Ion homeostasis / azurophil granule / retrograde trans-synaptic signaling by nitric oxide ...synaptic signaling by nitric oxide / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of hepatic stellate cell contraction / ROS and RNS production in phagocytes / negative regulation of iron ion transmembrane transport / negative regulation of vasoconstriction / Ion homeostasis / azurophil granule / retrograde trans-synaptic signaling by nitric oxide / negative regulation of cytosolic calcium ion concentration / positive regulation of sodium ion transmembrane transport / response to nitric oxide / postsynaptic specialization, intracellular component / postsynaptic density, intracellular component / positive regulation of the force of heart contraction / cadmium ion binding / behavioral response to cocaine / negative regulation of serotonin uptake / striated muscle contraction / peptidyl-cysteine S-nitrosylation / negative regulation of potassium ion transport / calyx of Held / regulation of sodium ion transport / negative regulation of calcium ion transport / negative regulation of insulin secretion / multicellular organismal response to stress / regulation of neurogenesis / sodium channel regulator activity / negative regulation of heart contraction / negative regulation of hydrolase activity / regulation of heart contraction / response to vitamin E / regulation of sensory perception of pain / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of blood pressure / cellular response to epinephrine stimulus / xenobiotic catabolic process / nitric oxide mediated signal transduction / sarcoplasmic reticulum membrane / vesicle membrane / T-tubule / nitric-oxide synthase activity / negative regulation of peptidyl-serine phosphorylation / NADPH binding / arginine catabolic process / response to hormone / photoreceptor inner segment / response to organonitrogen compound / positive regulation of histone acetylation / nitric oxide biosynthetic process / sarcoplasmic reticulum / response to activity / muscle contraction / response to nicotine / cell periphery / response to peptide hormone / female pregnancy / positive regulation of long-term synaptic potentiation / response to nutrient levels / secretory granule / sarcolemma / response to organic cyclic compound / response to lead ion / cellular response to growth factor stimulus / cellular response to mechanical stimulus / response to estrogen / Z disc / vasodilation / phosphoprotein binding / establishment of protein localization / positive regulation of neuron death / calcium-dependent protein binding / FMN binding / brain development / scaffold protein binding / flavin adenine dinucleotide binding / NADP binding / response to heat / transmembrane transporter binding / nuclear membrane / response to ethanol / positive regulation of peptidyl-serine phosphorylation / ATPase binding / response to lipopolysaccharide / aging / calmodulin binding / mitochondrial outer membrane / negative regulation of neuron apoptotic process / dendritic spine / response to hypoxia / postsynaptic density / cytoskeleton / oxidoreductase activity / negative regulation of cell population proliferation / glutamatergic synapse / membrane raft / synapse / dendrite
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 2 superfamily ...Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase (NOS) signature. / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal domain superfamily / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ferredoxin reductase-type FAD binding domain profile. / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / FAD-binding domain, ferredoxin reductase-type / Riboflavin synthase-like beta-barrel / PDZ domain / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-4E8 / ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / 5,6,7,8-TETRAHYDROBIOPTERIN / Nitric oxide synthase, brain
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.99 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Novel 2,4-Disubstituted Pyrimidines as Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase.
Authors: Mukherjee, P. / Li, H. / Sevrioukova, I. / Chreifi, G. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B.
History
DepositionOct 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references

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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)100,17511
Polymers97,6252
Non-polymers2,5509
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-86.5 kcal/mol
Surface area33140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.914, 110.816, 164.767
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 , 1 types, 2 molecules AB

#1: Protein NITRIC OXIDE SYNTHASE, BRAIN / / BNOS / CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S- ...BNOS / CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S-NITROSYLASE NOS1 / NEURONAL NITRIC OXIDE SYNTHASE


Mass: 48812.527 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, UNP RESIDUES 297-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH)

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Non-polymers , 6 types, 227 molecules

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


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


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#4: Chemical ChemComp-4E8 / 3-(3-fluorophenyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}propan-1-amine / N-2-(2-(1H-imidazol-1-yl)pyrimidin-4-yl)ethyl-3-(3-fluorophenyl)propan-1-amine


Mass: 325.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20FN5
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.1 %
Description: RMERGE GREATER THAN 1.00 RPIM 0.833 CC ONE HALF 0. 780
Crystal growpH: 5.8
Details: 20-24% PEG3350 0.1M MES 10% ETHYLENE GLYCOL 140-200 MM AMMONIUM ACETATE 5 MM GSH 35UM SDS, pH 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 65130 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 41.42 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.6
Reflection shellResolution: 1.99→2.03 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.99→92.12 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 14.33 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED RESIDUES 339 TO 349 IN CHAIN A AND 339 TO 347 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23893 3215 4.9 %RANDOM
Rwork0.18612 ---
obs0.18881 61865 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.072 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20 Å2
2---0.33 Å20 Å2
3----2.8 Å2
Refinement stepCycle: LAST / Resolution: 1.99→92.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 177 218 7054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197065
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9719617
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78623.874333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.729151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5831541
X-RAY DIFFRACTIONr_chiral_restr0.1220.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215441
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5253.1683278
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4244.7294093
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3023.3773787
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 184 -
Rwork0.338 3883 -
obs--85.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6251-0.0507-0.32841.0219-0.39114.1126-0.06530.09950.0338-0.0087-0.0170.08090.0964-0.2640.08230.1853-0.01240.01270.1486-0.01650.016411.3244.78722.589
20.809-0.147-0.09590.91940.33432.1392-0.0227-0.01560.0988-0.0977-0.0438-0.01560.09470.05120.06650.22840.00880.020.09450.00810.017312.3514.83260.056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A299 - 860
2X-RAY DIFFRACTION2B299 - 860

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