[English] 日本語
Yorodumi
- PDB-3n6f: Structure of endothelial nitric oxide synthase N368D single mutan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n6f
TitleStructure of endothelial nitric oxide synthase N368D single mutant heme domain complexed with 6,6'-(2,2'-(pyridine-3,5-diyl)bis(ethane-2,1-diyl))bis(4-methylpyridin-2-amine)
Components'Nitric oxide synthase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric oxide synthase / heme enzyme / substrate inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Nitric oxide stimulates guanylate cyclase / synaptic signaling by nitric oxide / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of vasoconstriction / ROS and RNS production in phagocytes / negative regulation of iron ion transmembrane transport / Ion homeostasis / azurophil granule / retrograde trans-synaptic signaling by nitric oxide ...Nitric oxide stimulates guanylate cyclase / synaptic signaling by nitric oxide / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of vasoconstriction / ROS and RNS production in phagocytes / negative regulation of iron ion transmembrane transport / Ion homeostasis / azurophil granule / retrograde trans-synaptic signaling by nitric oxide / negative regulation of cytosolic calcium ion concentration / response to nitric oxide / positive regulation of sodium ion transmembrane transport / postsynaptic specialization, intracellular component / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / cadmium ion binding / regulation of heart contraction / negative regulation of serotonin uptake / multicellular organismal response to stress / regulation of sodium ion transport / calyx of Held / behavioral response to cocaine / striated muscle contraction / sodium channel regulator activity / peptidyl-cysteine S-nitrosylation / postsynaptic density, intracellular component / negative regulation of calcium ion transport / regulation of neurogenesis / negative regulation of hydrolase activity / negative regulation of insulin secretion / 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 / vesicle membrane / negative regulation of peptidyl-serine phosphorylation / nitric-oxide synthase activity / NADPH binding / arginine catabolic process / response to organonitrogen compound / positive regulation of histone acetylation / response to hormone / sarcoplasmic reticulum / nitric oxide biosynthetic process / response to nicotine / response to peptide hormone / muscle contraction / response to activity / cell periphery / response to nutrient levels / secretory granule / positive regulation of long-term synaptic potentiation / photoreceptor inner segment / sarcolemma / response to organic cyclic compound / response to lead ion / cellular response to growth factor stimulus / Z disc / phosphoprotein binding / female pregnancy / establishment of protein localization / vasodilation / calcium-dependent protein binding / positive regulation of neuron death / cellular response to mechanical stimulus / FMN binding / brain development / scaffold protein binding / flavin adenine dinucleotide binding / response to heat / NADP binding / transmembrane transporter binding / nuclear membrane / positive regulation of peptidyl-serine phosphorylation / response to lipopolysaccharide / ATPase binding / response to estrogen / response to ethanol / mitochondrial outer membrane / negative regulation of neuron apoptotic process / calmodulin binding / dendritic spine / postsynaptic density / response to hypoxia / aging / cytoskeleton / oxidoreductase activity / negative regulation of cell population proliferation / glutamatergic synapse / synapse / membrane raft
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; 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 1 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal / Nitric oxide synthase (NOS) signature. ...Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; 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 1 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal / Nitric oxide synthase (NOS) signature. / Nitric oxide synthase, N-terminal domain superfamily / FAD binding domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / 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 / 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 / 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
ACETATE ION / CACODYLIC ACID / Chem-XFJ / PROTOPORPHYRIN IX CONTAINING FE / 5,6,7,8-TETRAHYDROBIOPTERIN / Nitric oxide synthase, brain
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,47615
Polymers99,4222
Non-polymers3,05413
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-126 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.986, 106.724, 157.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 'Nitric oxide synthase / Endothelial NOS / eNOS / EC-NOS / NOS type III / NOSIII / Constitutive NOS / cNOS


Mass: 49711.090 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)

-
Non-polymers , 8 types, 302 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-ACT / ACETATE ION / Acetate


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7AsO2
#6: 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
#7: Chemical ChemComp-XFJ / 6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine)


Mass: 347.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N5
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

-
Details

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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 48775 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 20.35
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.05 / Num. unique all: 2486 / Rsym value: 0.551 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.18→39.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.516 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R Free: 0.182 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21789 2557 5 %RANDOM
Rwork0.1781 ---
obs0.18008 48775 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.272 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.18→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 199 289 6910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226812
X-RAY DIFFRACTIONr_angle_refined_deg1.3529302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30123.375320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9671554
X-RAY DIFFRACTIONr_chiral_restr0.0820.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215324
X-RAY DIFFRACTIONr_mcbond_it0.5671.54036
X-RAY DIFFRACTIONr_mcangle_it1.09826512
X-RAY DIFFRACTIONr_scbond_it1.73132776
X-RAY DIFFRACTIONr_scangle_it2.8134.52790
LS refinement shellResolution: 2.179→2.235 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 180 -
Rwork0.271 3446 -
obs-3446 95.77 %
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)
10.6856-0.1644-0.331.24740.1811.48340.01820.01680.0173-0.25660.0565-0.1753-0.06950.1205-0.07470.083-0.04130.01770.099-0.0130.046710.91610.34132.137
20.8034-0.12320.25731.1195-0.71241.96970.0583-0.1472-0.08430.1350.05790.04470.0184-0.1304-0.11620.0289-0.017-0.00690.14250.00290.05042.9415.84567.972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 482
2X-RAY DIFFRACTION2B69 - 482

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more