- PDB-3nny: Structure of rat neuronal nitric oxide synthase heme domain compl... -
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Basic information
Entry
Database: PDB / ID: 3nny
Title
Structure of rat neuronal nitric oxide synthase heme domain complexed with 6-(((3R,4R)-4-(2-(3-Fluorophenethylamino)ethoxy)pyrrolidin-3-yl)methyl)pyridin-2-amine
Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport / response to nitric oxide / nitric oxide metabolic process / postsynaptic specialization, intracellular component / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Ion homeostasis / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / negative regulation of calcium ion transport / calyx of Held / behavioral response to cocaine / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase (NADPH) / sodium channel regulator activity / response to vitamin E / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / negative regulation of insulin secretion / nitric oxide mediated signal transduction / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / arginine catabolic process / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / sarcoplasmic reticulum membrane / T-tubule / cellular response to epinephrine stimulus / : / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to nutrient levels / potassium ion transport / response to hormone / sarcoplasmic reticulum / secretory granule / response to activity / positive regulation of long-term synaptic potentiation / establishment of localization in cell / cell periphery / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / establishment of protein localization / cellular response to mechanical stimulus / vasodilation / response to organic cyclic compound / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / response to estrogen / calcium-dependent protein binding / calcium ion transport / positive regulation of peptidyl-serine phosphorylation / FMN binding / ATPase binding / NADP binding / flavin adenine dinucleotide binding / nuclear membrane / response to heat / scaffold protein binding / response to ethanol / negative regulation of neuron apoptotic process / transmembrane transporter binding / mitochondrial outer membrane / response to lipopolysaccharide / dendritic spine / calmodulin binding / postsynaptic density / cytoskeleton / response to hypoxia / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / synapse / dendrite / heme binding / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II Similarity search - Function
Resolution: 2.1→38.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 12.524 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22267
2789
4.9 %
RANDOM
Rwork
0.1839
-
-
-
obs
0.18582
53969
99.15 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 55.83 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.19 Å2
0 Å2
0 Å2
2-
-
-0.1 Å2
0 Å2
3-
-
-
-0.09 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→38.22 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6657
0
181
293
7131
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
7043
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.294
1.992
9580
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.742
5
814
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.745
23.837
331
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.367
15
1166
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.308
15
41
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
992
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
5397
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.566
1.5
4081
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.065
2
6616
X-RAY DIFFRACTION
r_scbond_it
1.764
3
2962
X-RAY DIFFRACTION
r_scangle_it
2.715
4.5
2964
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.1→2.156 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.363
166
-
Rwork
0.297
3844
-
obs
-
3844
97.17 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
0.6081
-0.0882
-0.6301
0.7611
-0.1798
7.5029
-0.0334
0.1483
0.0004
-0.0563
-0.0815
0.0405
0.0664
-0.4918
0.1148
0.0569
0.0035
0.0093
0.1619
-0.0184
0.0771
11.481
4.697
22.583
2
0.7236
-0.1642
-0.2221
0.8243
0.3165
3.3467
-0.0285
-0.0518
0.0702
-0.0722
-0.05
-0.0067
0.0996
0.081
0.0784
0.0123
0.0206
0.0223
0.1046
0.0242
0.0861
12.29
4.805
59.891
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
299 - 860
2
X-RAY DIFFRACTION
2
B
299 - 860
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