[English] 日本語
Yorodumi
- PDB-3n6g: Structure of endothelial nitric oxide synthase N368D single mutan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n6g
TitleStructure of endothelial nitric oxide synthase N368D single mutant heme domain complexed with 4-(2-(5-(2-(6-amino-4-methylpyridin-2-yl)ethyl)pyridin-3-yl)ethyl)-6-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


positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis ...positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis / positive regulation of sodium ion transmembrane transport / response to nitric oxide / postsynaptic specialization, intracellular component / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / behavioral response to cocaine / postsynaptic density, intracellular component / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / calyx of Held / negative regulation of calcium ion transport / multicellular organismal response to stress / negative regulation of serotonin uptake / sodium channel regulator activity / regulation of neurogenesis / striated muscle contraction / negative regulation of insulin secretion / regulation of postsynaptic membrane potential / response to vitamin E / nitric-oxide synthase (NADPH) / xenobiotic catabolic process / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / NADPH binding / regulation of sodium ion transport / response to organonitrogen compound / T-tubule / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / negative regulation of peptidyl-serine phosphorylation / photoreceptor inner segment / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / response to nutrient levels / response to activity / response to nicotine / muscle contraction / sarcoplasmic reticulum / establishment of localization in cell / secretory granule / positive regulation of long-term synaptic potentiation / female pregnancy / cell periphery / response to lead ion / sarcolemma / establishment of protein localization / potassium ion transport / response to organic cyclic compound / response to peptide hormone / Z disc / phosphoprotein binding / vasodilation / cellular response to growth factor stimulus / cellular response to mechanical stimulus / response to estrogen / calcium-dependent protein binding / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / ATPase binding / response to heat / scaffold protein binding / response to ethanol / nuclear membrane / negative regulation of neuron apoptotic process / mitochondrial outer membrane / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia / calmodulin binding / cytoskeleton / membrane raft / negative regulation of cell population proliferation / dendrite / glutamatergic synapse / synapse / heme binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex
Similarity search - Function
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;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily ...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;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain 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 / 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 / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-XFK / Nitric oxide synthase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.21 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-125 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.742, 106.414, 156.889
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, 247 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-XFK / 6-(2-{5-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-3-yl}ethyl)-4-methylpyridin-2-amine


Mass: 347.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N5
#6: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7AsO2
#7: 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
#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.: 234 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsAUTHORS STATE THAT THEIR DENSITY SUPPORTS THAT THE RESIDUE IS ARG AND NOT CYS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.26 %
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: 2.22→50 Å / Num. obs: 49005 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 20.57
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 1.87 / Num. unique all: 2346 / Rsym value: 0.705 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.21→32.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.468 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R Free: 0.206 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23793 2437 5 %RANDOM
Rwork0.18689 ---
obs0.18942 46518 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.052 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.42 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.21→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 0 199 234 6869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226842
X-RAY DIFFRACTIONr_angle_refined_deg1.43629346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22323.364321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.488151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4531554
X-RAY DIFFRACTIONr_chiral_restr0.0850.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215352
X-RAY DIFFRACTIONr_mcbond_it0.6031.54054
X-RAY DIFFRACTIONr_mcangle_it1.14726544
X-RAY DIFFRACTIONr_scbond_it1.92132788
X-RAY DIFFRACTIONr_scangle_it3.0564.52802
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 155 -
Rwork0.298 3067 -
obs-3067 89.97 %
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)
10.7136-0.2016-0.33951.08940.13921.50550.0150.0030.0091-0.18210.0318-0.1436-0.06160.1265-0.04690.0496-0.03390.00520.1909-0.00830.158811.08210.32132.028
20.6891-0.21690.24551.0962-0.72472.03540.0459-0.1245-0.08480.08480.06070.07250.038-0.123-0.10660.0173-0.0130.0010.23420.0030.17592.765.82467.897
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 482
2X-RAY DIFFRACTION2B69 - 482

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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