- PDB-4c39: Structure of rat neuronal nitric oxide synthase heme domain in co... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4c39
Title
Structure of rat neuronal nitric oxide synthase 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
Components
NITRIC OXIDE SYNTHASE, BRAIN
Keywords
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 / 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) / multicellular organismal response to stress / xenobiotic catabolic process / nitric-oxide synthase activity / negative regulation of peptidyl-serine phosphorylation / nitric oxide mediated signal transduction / arginine catabolic process / NADPH binding / regulation of sodium ion transport / response to organonitrogen compound / sarcoplasmic reticulum membrane / T-tubule / cellular response to epinephrine stimulus / 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 / secretory granule / female pregnancy / positive regulation of long-term synaptic potentiation / cell periphery / establishment of localization in cell / phosphoprotein binding / response to lead ion / sarcolemma / establishment of protein localization / potassium ion transport / response to organic cyclic compound / response to peptide hormone / cellular response to growth factor stimulus / Z disc / vasodilation / 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 / cytoskeleton / calmodulin binding / 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
NITRICOXIDESYNTHASE, 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: 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, 348 molecules
#2: Chemical
ChemComp-HEM / PROTOPORPHYRINIXCONTAININGFE / HEME / Heme B
Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979 Å / Relative weight: 1
Reflection
Resolution: 1.98→50 Å / Num. obs: 66939 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.8
Reflection shell
Resolution: 1.98→2.01 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6
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Processing
Software
Name
Version
Classification
REFMAC
5.6.0117
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
REFMAC
phasing
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.98→92.19 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.135 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. RESIDUES 339 TO 349 IN CHAIN A AND 339-347 IN CHAIN B ARE DISORDERED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2279
3294
4.9 %
RANDOM
Rwork
0.18057
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obs
0.18294
63550
99.61 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK