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- PDB-5fvx: Structure of human nNOS R354A G357D mutant heme domain in complex... -

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Basic information

Entry
Database: PDB / ID: 5fvx
TitleStructure of human nNOS R354A G357D mutant heme domain in complex with with 6-(2-(5-(3-(DIMETHYLAMINO)PROPYL) PYRIDIN-3-YL)ETHYL)-4-METHYLPYRIDIN-2-AMINE
ComponentsNITRIC OXIDE SYNTHASE, BRAIN
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE
Function / homology
Function and homology information


positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of calcium ion transport into cytosol / myoblast fusion / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide ...positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of calcium ion transport into cytosol / myoblast fusion / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport / 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 / negative regulation of serotonin uptake / sodium channel regulator activity / striated muscle contraction / nitric-oxide synthase (NADPH) / regulation of cardiac muscle contraction / multicellular organismal response to stress / xenobiotic catabolic process / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / regulation of sodium ion transport / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / photoreceptor inner segment / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / cell redox homeostasis / muscle contraction / sarcoplasmic reticulum / cell periphery / sarcolemma / cellular response to growth factor stimulus / vasodilation / calcium-dependent protein binding / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / response to heat / scaffold protein binding / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia / cytoskeleton / calmodulin binding / membrane raft / synapse / heme binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 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, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain 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
5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-W67 / Nitric oxide synthase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibition by Optimization of the 2-Aminopyridine-Based Scaffold with a Pyridine Linker.
Authors: Wang, H. / Qin, Y. / Li, H. / Roman, L.J. / Martasek, P. / Poulos, T.L. / Silverman, R.B.
History
DepositionFeb 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references

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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)99,9479
Polymers97,5692
Non-polymers2,3787
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint-84.4 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.490, 122.110, 164.070
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 / / CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S- ...CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S-NITROSYLASE NOS1 / BNOS / NEURONAL NITRIC OXIDE SYNTHASE


Mass: 48784.496 Da / Num. of mol.: 2 / Fragment: RESIDUES 302-722 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29475

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Non-polymers , 5 types, 290 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#4: Chemical ChemComp-W67 / 6-(2-(5-(3-(DIMETHYLAMINO)PROPYL)PYRIDIN-3-YL)ETHYL)-4-METHYLPYRIDIN-2-AMINE


Mass: 298.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26N4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.74 Å3/Da / Density % sol: 50.7 %
Description: OVERALL RMERGE 0.365 RPIM 0.253 CC ONE HALF 0.984 HIGHEST RESOLUTION SHELL RMERGE 3.771 RPIM 2.653 CC ONE HALF 0.274
Crystal growpH: 6.2
Details: 8-9% PEG3350 40 MM CITRIC ACID 60 MM BISTRISPROPANE 10% GLYCEROL 5 MM TCEP, pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 45518 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 33.24 Å2 / Rmerge(I) obs: 0.36 / Net I/σ(I): 5.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.8 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.3→82.035 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 30.93 / Stereochemistry target values: ML
Details: RESIDUES 342 TO 351 IN CHAIN A AND 343 TO 353 IN CHAIN B ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2593 4240 4.9 %
Rwork0.1992 --
obs0.2021 45427 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→82.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6699 0 165 283 7147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077094
X-RAY DIFFRACTIONf_angle_d1.1769656
X-RAY DIFFRACTIONf_dihedral_angle_d15.262582
X-RAY DIFFRACTIONf_chiral_restr0.072999
X-RAY DIFFRACTIONf_plane_restr0.0051220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32620.36961360.34092789X-RAY DIFFRACTION99
2.3262-2.35350.45331500.34162789X-RAY DIFFRACTION98
2.3535-2.38230.41391570.33022793X-RAY DIFFRACTION95
2.3823-2.41240.3891630.32572763X-RAY DIFFRACTION98
2.4124-2.44420.35831490.332788X-RAY DIFFRACTION98
2.4442-2.47760.39091490.3312795X-RAY DIFFRACTION97
2.4776-2.5130.34281740.30732752X-RAY DIFFRACTION96
2.513-2.55050.33831370.29332778X-RAY DIFFRACTION98
2.5505-2.59040.35761370.28632793X-RAY DIFFRACTION97
2.5904-2.63290.34771450.2772705X-RAY DIFFRACTION95
2.6329-2.67830.30841700.28122783X-RAY DIFFRACTION98
2.6783-2.7270.32381440.27092769X-RAY DIFFRACTION97
2.727-2.77940.34771190.2642813X-RAY DIFFRACTION95
2.7794-2.83620.37941210.25542787X-RAY DIFFRACTION98
2.8362-2.89780.28171270.24132747X-RAY DIFFRACTION95
2.8978-2.96530.25931560.24682757X-RAY DIFFRACTION97
2.9653-3.03940.33411200.23392768X-RAY DIFFRACTION96
3.0394-3.12160.2931480.22092697X-RAY DIFFRACTION95
3.1216-3.21350.27651420.22342770X-RAY DIFFRACTION97
3.2135-3.31720.30921270.20722725X-RAY DIFFRACTION94
3.3172-3.43570.26261400.19212745X-RAY DIFFRACTION96
3.4357-3.57330.26791450.17482696X-RAY DIFFRACTION94
3.5733-3.73590.23271560.15712680X-RAY DIFFRACTION93
3.7359-3.93290.21011470.15332704X-RAY DIFFRACTION95
3.9329-4.17930.22431450.13572658X-RAY DIFFRACTION93
4.1793-4.5020.16581410.13062673X-RAY DIFFRACTION93
4.502-4.9550.15171320.122649X-RAY DIFFRACTION92
4.955-5.67180.17441270.13642659X-RAY DIFFRACTION93
5.6718-7.14520.21381410.14592656X-RAY DIFFRACTION92
7.1452-82.08720.1671950.14182615X-RAY DIFFRACTION90
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)
10.9335-0.2605-0.23611.11220.35513.9432-0.0165-0.04970.0357-0.0592-0.0805-0.01220.22180.2320.07940.1654-0.01780.02780.25890.04610.2757117.7588249.1019358.6741
20.9657-0.0812-0.78711.33250.28256.83590.03520.192-0.0111-0.0971-0.13630.07830.0106-0.5210.03950.21680.0210.00870.3285-0.02630.2768116.5228248.0798321.5995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 302:721)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 304:721)

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