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- PDB-3b3p: Structure of neuronal nos heme domain in complex with a inhibitor... -

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Basic information

Entry
Database: PDB / ID: 3b3p
TitleStructure of neuronal nos heme domain in complex with a inhibitor (+-)-n1-{cis-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}-n2-(4'-chlorobenzyl)ethane-1,2-diamine
ComponentsNitric-oxide synthase
KeywordsOXIDOREDUCTASE / nitric oxide synthase / heme enzyme / inhibitor / Alternative splicing / Calmodulin-binding / Cell projection / FAD / FMN / Iron / Membrane / Metal-binding / NADP
Function / homology
Function and homology information


negative regulation of hepatic stellate cell contraction / retrograde trans-synaptic signaling by nitric oxide / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / positive regulation of sodium ion transmembrane transport / negative regulation of vasoconstriction ...negative regulation of hepatic stellate cell contraction / retrograde trans-synaptic signaling by nitric oxide / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / positive regulation of sodium ion transmembrane transport / negative regulation of vasoconstriction / peptidyl-cysteine S-nitrosylation / postsynaptic specialization, intracellular component / nitric oxide metabolic process / negative regulation of cytosolic calcium ion concentration / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Ion homeostasis / response to nitric oxide / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / negative regulation of calcium ion transport / behavioral response to cocaine / nitric oxide mediated signal transduction / regulation of neurogenesis / nitric-oxide synthase (NADPH) / negative regulation of serotonin uptake / sodium channel regulator activity / response to vitamin E / regulation of postsynaptic membrane potential / nitric-oxide synthase activity / postsynaptic density, intracellular component / multicellular organismal response to stress / arginine catabolic process / negative regulation of insulin secretion / xenobiotic catabolic process / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / negative regulation of blood pressure / response to hormone / T-tubule / photoreceptor inner segment / cellular response to epinephrine stimulus / sarcoplasmic reticulum membrane / nitric oxide biosynthetic process / calyx of Held / sarcoplasmic reticulum / secretory granule / positive regulation of long-term synaptic potentiation / cell periphery / response to activity / female pregnancy / establishment of localization in cell / phosphoprotein binding / response to nicotine / establishment of protein localization / response to lead ion / response to nutrient levels / potassium ion transport / sarcolemma / cellular response to growth factor stimulus / : / caveola / response to peptide hormone / Z disc / cellular response to mechanical stimulus / response to estrogen / vasodilation / calcium-dependent protein binding / calcium ion transport / FMN binding / NADP binding / flavin adenine dinucleotide binding / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / response to ethanol / response to lipopolysaccharide / negative regulation of neuron apoptotic process / dendritic spine / mitochondrial outer membrane / transmembrane transporter binding / response to hypoxia / cytoskeleton / calmodulin binding / postsynaptic density / membrane raft / negative regulation of cell population proliferation / dendrite / heme binding / 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 / 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, 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 / 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 / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-JI7 / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsIgarashi, J. / Li, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Crystal structures of constitutive nitric oxide synthases in complex with de novo designed inhibitors.
Authors: Igarashi, J. / Li, H. / Jamal, J. / Ji, H. / Fang, J. / Lawton, G.R. / Silverman, R.B. / Poulos, T.L.
History
DepositionOct 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: Nitric-oxide synthase
B: Nitric-oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,27211
Polymers97,6252
Non-polymers2,6479
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.580, 110.250, 164.390
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 / NOS type I / Neuronal NOS / N-NOS / nNOS / Constitutive NOS / NC-NOS / BNOS


Mass: 48812.527 Da / Num. of mol.: 2 / Fragment: residues 297-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / 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, 256 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#6: Chemical ChemComp-JI7 / N-{(3R,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-(3-chlorobenzyl)ethane-1,2-diamine / (+-)-N1-{trans-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}-N2-(3'-chlorobenzyl)ethane-1,2-diamine


Mass: 373.923 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28ClN5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG3350, MES, ammonium acetate, GSH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 35031 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 6.3
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.592 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.45→38.86 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2201651.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1747 5 %RANDOM
Rwork0.209 ---
obs0.209 34892 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5526 Å2 / ksol: 0.364993 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1-31.84 Å20 Å20 Å2
2---8.01 Å20 Å2
3----23.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.45→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6676 0 181 247 7104
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 293 5.1 %
Rwork0.374 5469 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2hetero.parhetero.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ji4.parji4.top

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