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- PDB-1vag: Neuronal nitric oxide synthase oxygenase domain complexed with th... -

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Basic information

Entry
Database: PDB / ID: 1vag
TitleNeuronal nitric oxide synthase oxygenase domain complexed with the inhibitor AR-R17477
ComponentsNitric-oxide synthase, brain
KeywordsOXIDOREDUCTASE / RAT NNOSOXY COMPLEX WITH AR-R17477
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 / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / response to vitamin B3 / azurophil granule / postsynaptic specialization, intracellular component / negative regulation of vasoconstriction ...negative regulation of hepatic stellate cell contraction / 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 / response to vitamin B3 / azurophil granule / postsynaptic specialization, intracellular component / negative regulation of vasoconstriction / negative regulation of cytosolic calcium ion concentration / Ion homeostasis / response to nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of sodium ion transmembrane transport / peptidyl-cysteine S-nitrosylase activity / regulation of postsynaptic membrane potential / cadmium ion binding / positive regulation of the force of heart contraction / behavioral response to cocaine / negative regulation of potassium ion transport / negative regulation of calcium ion transport / regulation of neurogenesis / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / sodium channel regulator activity / response to vitamin E / negative regulation of serotonin uptake / postsynaptic density, intracellular component / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / L-arginine catabolic process / negative regulation of insulin secretion / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / nitric oxide metabolic process / negative regulation of blood pressure / response to hormone / sarcoplasmic reticulum membrane / photoreceptor inner segment / cellular response to epinephrine stimulus / T-tubule / nitric oxide biosynthetic process / calyx of Held / secretory granule / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / response to activity / cell periphery / female pregnancy / establishment of localization in cell / phosphoprotein binding / response to nicotine / establishment of protein localization / response to nutrient levels / response to lead ion / potassium ion transport / : / sarcolemma / cellular response to growth factor stimulus / caveola / response to peptide hormone / Z disc / response to estrogen / cellular response to mechanical stimulus / calcium ion transport / calcium-dependent protein binding / vasodilation / FMN binding / flavin adenine dinucleotide binding / NADP binding / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / dendritic spine / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / cytoskeleton / response to hypoxia / calmodulin binding / postsynaptic density / membrane raft / negative regulation of cell population proliferation / synapse / heme binding / dendrite / 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. / PDZ domain / 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-ARR / 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 Å
AuthorsFedorov, R. / Vasan, R. / Ghosh, D.K. / Schlichting, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structures of nitric oxide synthase isoforms complexed with the inhibitor AR-R17477 suggest a rational basis for specificity and inhibitor design
Authors: Fedorov, R. / Vasan, R. / Ghosh, D.K. / Schlichting, I.
History
DepositionFeb 16, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8735
Polymers48,5801
Non-polymers1,2934
Water4,161231
1
A: Nitric-oxide synthase, brain
hetero molecules

A: Nitric-oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,74710
Polymers97,1602
Non-polymers2,5868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11040 Å2
ΔGint-151 kcal/mol
Surface area33790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)45.269, 109.199, 164.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-950-

ZN

21A-209-

HOH

31A-218-

HOH

DetailsThe second part of the biological assembly is generated by the symmetry operation: -x, y, -z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitric-oxide synthase, brain / NOS / type I / Neuronal NOS / N-NOS / NNOS / Constitutive NOS / NC-NOS / BNOS


Mass: 48580.203 Da / Num. of mol.: 1
Fragment: neuronal oxide synthase oxygenase domain (residues 297-716)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NOS1, BNOS / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / References: UniProt: P29476, nitric-oxide synthase (NADPH)

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Non-polymers , 5 types, 235 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#5: Chemical ChemComp-ARR / N-(4-{2-[(3-CHLOROBENZYL)AMINO]ETHYL}PHENYL)THIOPHENE-2-CARBOXIMIDAMIDE / N-(4-(2-((3-CHLOROPHENYLMETHYL)AMINO)ETHYL)PHENYL)-2-THIOPHECARBOXAMIDINE


Mass: 369.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20ClN3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 1.95 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, DTT, PEG3350, EPPS, NACL, GLYCEROL, beta-MERCAPTOETHANOL, AR-R17477, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.969 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 26980 / Num. obs: 26632 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.091 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.346 / % possible all: 91.4

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Processing

Software
NameVersionClassification
ProDCdata collection
XDSdata reduction
AMoREphasing
CNS1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QW6

1qw6


Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.229 1362 random
Rwork0.193 --
all0.1948 26560 -
obs0.1948 26560 -
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 86 231 3735

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