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- PDB-4cx6: Structure of rat neuronal nitric oxide synthase H341L mutant heme... -

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Basic information

Entry
Database: PDB / ID: 4cx6
TitleStructure of rat neuronal nitric oxide synthase H341L mutant heme domain in complex with 6-((((3S, 5R)-5-(((6-AMINO-4-METHYLPYRIDIN-2- YL)METHOXY)METHYL)PYRROLIDIN-3-YL)OXY)METHYL)-4-METHYLPYRIDIN-2-AMINE
ComponentsNITRIC OXIDE SYNTHASE, BRAIN
KeywordsOXIDOREDUCTASE / 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 / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of cytosolic calcium ion concentration / 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 / regulation of neurogenesis / negative regulation of serotonin uptake / 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 / regulation of sodium ion transport / negative regulation of blood pressure / response to hormone / behavioral response to cocaine / nitric oxide metabolic process / nitric oxide biosynthetic process / photoreceptor inner segment / T-tubule / cellular response to epinephrine stimulus / 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 / response to nutrient levels / phosphoprotein binding / establishment of protein localization / establishment of localization in cell / cellular response to mechanical stimulus / female pregnancy / 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 / NADP binding / flavin adenine dinucleotide 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / mitochondrial outer membrane / cytoskeleton / calmodulin binding / response to hypoxia / postsynaptic density / membrane raft / negative regulation of cell population proliferation / heme binding / synapse / 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
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
ACETATE ION / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-Q16 / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2014
Title: Mobility of a Conserved Tyrosine Residue Controls Isoform-Dependent Enzyme-Inhibitor Interactions in Nitric Oxide Synthases.
Authors: Li, H. / Jamal, J. / Delker, S.L. / Plaza, C. / Ji, H. / Jing, Q. / Huang, H. / Kang, S. / Silverman, R.B. / Poulos, T.L.
History
DepositionApr 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.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_asym_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.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.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

Downloads & links

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE, BRAIN
B: NITRIC OXIDE SYNTHASE, BRAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,18911
Polymers97,5752
Non-polymers2,6149
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-123.8 kcal/mol
Surface area33150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.982, 110.707, 164.386
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, BRAIN / BNOS / CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S- ...BNOS / CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S-NITROSYLASE NOS1


Mass: 48787.535 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, RESIDUES 297-718 / Mutation: YES
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, 391 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-Q16 / 6-((((3S, 5R)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine


Mass: 357.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N5O2
#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.: 382 / 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: 2.47 Å3/Da / Density % sol: 50.2 % / Description: NONE
Crystal growpH: 5.8
Details: 20-22% PEG3350 0.1 MES PH 5.8 140-200MM AMMONIUM ACETATE 10% ETHYLENE GLYCOL 35UM SDS 5MM GSH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 75577 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 25.34 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→37.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.418 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED RESIDUES 339 TO 349 IN CHAIN A AND 339-347 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 3742 5 %RANDOM
Rwork0.18457 ---
obs0.18617 71736 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.305 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å20 Å20 Å2
2--0.63 Å20 Å2
3----3.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 181 382 7222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9729616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17823.855332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.692151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7791541
X-RAY DIFFRACTIONr_chiral_restr0.0950.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215425
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 274 -
Rwork0.288 5262 -
obs--99.91 %
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)
10.4557-0.0767-0.5160.6842-0.38945.6448-0.06220.11430.0051-0.0332-0.03040.04020.0718-0.38250.09270.0163-0.01040.01250.1083-0.01410.06911.34.71122.535
20.7115-0.153-0.13840.75660.3262.6467-0.034-0.0340.0748-0.0841-0.0498-0.00690.08020.07310.08380.02210.01670.01460.06130.01480.068612.364.74759.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A299 - 860
2X-RAY DIFFRACTION2B299 - 860

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