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- PDB-3n6d: Structure of endothelial nitric oxide synthase H373S single mutan... -

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Basic information

Entry
Database: PDB / ID: 3n6d
TitleStructure of endothelial nitric oxide synthase H373S single mutant heme domain complexed with 6,6'-(2,2'-(5-amino-1,3-phenylene)bis(ethane-2,1-diyl))bis(4-methylpyridin-2-amine)
ComponentsNitric oxide synthase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric oxide synthase / heme enzyme / substrate inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE 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 / negative regulation of vasoconstriction / ROS and RNS production in phagocytes / negative regulation of iron ion transmembrane transport / azurophil granule / Ion homeostasis / 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 / negative regulation of vasoconstriction / ROS and RNS production in phagocytes / negative regulation of iron ion transmembrane transport / azurophil granule / Ion homeostasis / retrograde trans-synaptic signaling by nitric oxide / negative regulation of cytosolic calcium ion concentration / behavioral response to cocaine / response to nitric oxide / positive regulation of sodium ion transmembrane transport / postsynaptic specialization, intracellular component / positive regulation of the force of heart contraction / regulation of heart contraction / negative regulation of potassium ion transport / cadmium ion binding / postsynaptic density, intracellular component / negative regulation of serotonin uptake / calyx of Held / regulation of sodium ion transport / sodium channel regulator activity / striated muscle contraction / peptidyl-cysteine S-nitrosylation / negative regulation of calcium ion transport / negative regulation of insulin secretion / regulation of neurogenesis / negative regulation of hydrolase activity / multicellular organismal response to stress / response to vitamin E / xenobiotic catabolic process => GO:0042178 / negative regulation of heart contraction / regulation of sensory perception of pain / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of blood pressure / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / T-tubule / nitric oxide mediated signal transduction / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / negative regulation of peptidyl-serine phosphorylation / nitric-oxide synthase activity / vesicle membrane / arginine catabolic process / NADPH binding / response to organonitrogen compound / response to hormone / positive regulation of histone acetylation / sarcoplasmic reticulum / response to peptide hormone / nitric oxide biosynthetic process / response to nicotine / response to nutrient levels / response to activity / cell periphery / secretory granule / positive regulation of long-term synaptic potentiation / photoreceptor inner segment / sarcolemma / muscle contraction / cellular response to growth factor stimulus / response to organic cyclic compound / vasodilation / response to lead ion / female pregnancy / Z disc / phosphoprotein binding / establishment of protein localization / calcium-dependent protein binding / positive regulation of neuron death / cellular response to mechanical stimulus / brain development / FMN binding / scaffold protein binding / flavin adenine dinucleotide binding / response to heat / transmembrane transporter binding / NADP binding / nuclear membrane / positive regulation of peptidyl-serine phosphorylation / response to lipopolysaccharide / ATPase binding / mitochondrial outer membrane / response to ethanol / negative regulation of neuron apoptotic process / response to estrogen / calmodulin binding / dendritic spine / aging / response to hypoxia / postsynaptic density / cytoskeleton / oxidoreductase activity / negative regulation of cell population proliferation / synapse / glutamatergic synapse / membrane raft
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; Chain A, domain 1 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal ...Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; Chain A, domain 1 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal / Nitric oxide synthase (NOS) signature. / FAD binding domain / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Oxidoreductase NAD-binding domain / Oxidoreductase FAD/NAD(P)-binding / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / 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
CACODYLIC ACID / 5,6,7,8-TETRAHYDROBIOPTERIN / Chem-XFN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase, brain
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.05 Å
AuthorsDelker, S.L. / Li, H. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2010
Title: Role of zinc in isoform-selective inhibitor binding to neuronal nitric oxide synthase .
Authors: Delker, S.L. / Xue, F. / Li, H. / Jamal, J. / Silverman, R.B. / Poulos, T.L.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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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)102,09811
Polymers99,3182
Non-polymers2,7809
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-125 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.224, 106.669, 156.785
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 / / Endothelial NOS / eNOS / EC-NOS / NOS type III / NOSIII / Constitutive NOS / cNOS


Mass: 49659.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: NOS3 / Plasmid: pCWori / 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, 30 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-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7AsO2
#5: Chemical ChemComp-XFN / 6,6'-[(5-aminobenzene-1,3-diyl)diethane-2,1-diyl]bis(4-methylpyridin-2-amine)


Mass: 361.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N5
#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.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THEIR DENSITY SUPPORT ARG AT THIS POSITION.

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 9-12% PEG 3350, 0.2M magnesium acetate, 0.1M sodium cacodylate, 0.005M TCEP-HCl , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 21, 2010 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 18759 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 11.88
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.95 / Num. unique all: 931 / Rsym value: 0.702 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.05→38.59 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.861 / SU B: 58.282 / SU ML: 0.488 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R Free: 0.55 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28921 922 4.9 %RANDOM
Rwork0.19869 ---
obs0.20323 17785 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.468 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 3.05→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 181 21 6612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226785
X-RAY DIFFRACTIONr_angle_refined_deg1.70429273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7725803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29823.438317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.288151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7031553
X-RAY DIFFRACTIONr_chiral_restr0.1090.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215301
X-RAY DIFFRACTIONr_mcbond_it0.5191.54037
X-RAY DIFFRACTIONr_mcangle_it1.01526514
X-RAY DIFFRACTIONr_scbond_it1.57832748
X-RAY DIFFRACTIONr_scangle_it2.7454.52759
LS refinement shellResolution: 3.054→3.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 60 -
Rwork0.265 1250 -
obs-1250 96.04 %
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)
10.82-0.0955-0.44481.47310.34542.1352-0.01550.05350.0162-0.30070.1319-0.2023-0.06680.125-0.11640.0841-0.07620.0120.2674-0.01350.308310.91910.51631.739
21.4079-0.38210.4871.4192-0.98392.6432-0.0362-0.1374-0.11560.12290.09240.0251-0.0691-0.1334-0.05630.0501-0.06570.00730.2804-0.01530.30292.8295.90367.934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 482
2X-RAY DIFFRACTION2B69 - 482

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