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

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Basic information

Entry
Database: PDB / ID: 4ugz
TitleStructure of rat neuronal nitric oxide synthase heme domain in complex with N1-(3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)phenyl)-N1, N2-dimethylethane-1,2-diamine
ComponentsNEURONAL NITRIC OXIDE SYNTHASE
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of hepatic stellate cell contraction / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / postsynaptic specialization, intracellular component / ROS and RNS production in phagocytes / azurophil granule / synaptic signaling by nitric oxide / Ion homeostasis ...negative regulation of hepatic stellate cell contraction / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / postsynaptic specialization, intracellular component / ROS and RNS production in phagocytes / azurophil granule / synaptic signaling by nitric oxide / Ion homeostasis / negative regulation of vasoconstriction / response to nitric oxide / negative regulation of cytosolic calcium ion concentration / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / response to vitamin E / positive regulation of sodium ion transmembrane transport / peptidyl-cysteine S-nitrosylase activity / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of calcium ion transport / negative regulation of potassium ion transport / regulation of postsynaptic membrane potential / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / sodium channel regulator activity / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / L-arginine catabolic process / postsynaptic density, intracellular component / NADPH binding / striated muscle contraction / nitric oxide-cGMP-mediated signaling / behavioral response to cocaine / regulation of sodium ion transport / negative regulation of blood pressure / response to hormone / nitric oxide metabolic process / nitric oxide biosynthetic process / photoreceptor inner segment / cellular response to epinephrine stimulus / T-tubule / sarcoplasmic reticulum membrane / secretory granule / calyx of Held / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / response to activity / cell periphery / response to nicotine / phosphoprotein binding / response to nutrient levels / establishment of localization in cell / establishment of protein localization / female pregnancy / cellular response to mechanical stimulus / negative regulation of insulin secretion / response to peptide hormone / sarcolemma / caveola / cellular response to growth factor stimulus / potassium ion transport / response to lead ion / response to estrogen / vasodilation / Z disc / calcium-dependent protein binding / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / NADP binding / positive regulation of neuron apoptotic process / response to heat / ATPase binding / scaffold protein binding / response to ethanol / nuclear membrane / response to lipopolysaccharide / dendritic spine / negative regulation of neuron apoptotic process / transmembrane transporter binding / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / cytoskeleton / calmodulin binding / response to hypoxia / postsynaptic density / membrane raft / negative regulation of cell population proliferation / heme binding / dendrite / synapse / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II
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, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 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, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 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 / PDZ 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 / 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-4V4 / ACETATE ION / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.076 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: 2-Aminopyridines with a Truncated Side Chain to Improve Human Neuronal Nitric Oxide Synthase Inhibitory Potency and Selectivity.
Authors: Kang, S. / Li, H. / Tang, W. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B.
History
DepositionMar 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURONAL NITRIC OXIDE SYNTHASE
B: NEURONAL NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,12111
Polymers97,6252
Non-polymers2,4969
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-84 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.872, 111.230, 164.875
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 NEURONAL NITRIC OXIDE SYNTHASE


Mass: 48812.527 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, 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, 265 molecules

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


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


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Chemical ChemComp-4V4 / N1-(3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)phenyl)-N1,N2-dimethylethane-1,2-diamine


Mass: 298.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26N4
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: RPIM 0.721 CC ONE HALF 0.575
Crystal growpH: 5.8
Details: 20-22% PEG3350 0.1M MES, PH5.8 140-200 MM AMMONIUM ACETATE 10% ETHYLENE GLYCOL 5 MM GSH 30UM SDS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 57430 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 39.85 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.5
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.8 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OM4

1om4


Resolution: 2.076→40.838 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 30.29 / Stereochemistry target values: ML
Details: RESIDUES 339 TO 349 IN CHAIN A AND 339 TO 347 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2274 2826 4.9 %
Rwork0.1877 --
obs0.1897 57220 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.076→40.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 173 256 7088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087050
X-RAY DIFFRACTIONf_angle_d1.1399596
X-RAY DIFFRACTIONf_dihedral_angle_d15.292564
X-RAY DIFFRACTIONf_chiral_restr0.072991
X-RAY DIFFRACTIONf_plane_restr0.0051214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0763-2.11210.417960.3111943X-RAY DIFFRACTION71
2.1121-2.15050.34091080.2952612X-RAY DIFFRACTION94
2.1505-2.19180.37461260.28222673X-RAY DIFFRACTION97
2.1918-2.23660.35211400.26672695X-RAY DIFFRACTION98
2.2366-2.28520.30791710.25852661X-RAY DIFFRACTION98
2.2852-2.33830.30571570.24322726X-RAY DIFFRACTION99
2.3383-2.39680.30291300.24352721X-RAY DIFFRACTION100
2.3968-2.46160.32581360.23372802X-RAY DIFFRACTION100
2.4616-2.5340.30251400.23052726X-RAY DIFFRACTION100
2.534-2.61580.24661490.21422758X-RAY DIFFRACTION100
2.6158-2.70930.23931280.21222778X-RAY DIFFRACTION100
2.7093-2.81770.23111390.21272756X-RAY DIFFRACTION100
2.8177-2.94590.29661460.21192765X-RAY DIFFRACTION100
2.9459-3.10120.26741580.21492759X-RAY DIFFRACTION100
3.1012-3.29540.25031350.20642788X-RAY DIFFRACTION100
3.2954-3.54970.20481430.17992797X-RAY DIFFRACTION100
3.5497-3.90670.22631640.16232783X-RAY DIFFRACTION100
3.9067-4.47140.18191400.15052820X-RAY DIFFRACTION99
4.4714-5.63120.18061660.14512840X-RAY DIFFRACTION100
5.6312-40.84550.17171540.16282991X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8831-0.1721-0.66031.3297-0.07987.255-0.00530.180.01080.0548-0.10510.05240.0265-0.46680.03510.1004-0.0148-0.00710.1677-0.00330.216111.29394.790722.6401
21.017-0.2424-0.03761.08340.44753.8734-0.03320.02220.0893-0.1628-0.09650.02630.15210.07510.07050.08030.03840.04420.14320.01750.225312.31554.890160.1426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 299:716)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 299:718)

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