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- PDB-5vv7: Structure of bovine endothelial nitric oxide synthase heme domain... -

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Basic information

Entry
Database: PDB / ID: 5vv7
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 7-(((3-(Pyridin-3-yl)propyl)amino)methyl)quinolin-2-amine
ComponentsNitric oxide synthase, endothelial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric oxide synthase / inhibitor complex / heme enzyme / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric-oxide synthase activity / mitochondrion organization / arginine catabolic process / nitric oxide biosynthetic process / caveola ...cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric-oxide synthase activity / mitochondrion organization / arginine catabolic process / nitric oxide biosynthetic process / caveola / FMN binding / blood coagulation / flavin adenine dinucleotide binding / NADP binding / calmodulin binding / cytoskeleton / heme binding / Golgi apparatus / metal ion binding
Similarity search - Function
Nitric-oxide synthase, eukaryote / 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, N-terminal domain superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, oxygenase domain ...Nitric-oxide synthase, eukaryote / 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, N-terminal domain superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / FAD-binding domain, ferredoxin reductase-type / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-XH8 / Nitric oxide synthase, endothelial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsLi, H. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Hydrophilic, Potent, and Selective 7-Substituted 2-Aminoquinolines as Improved Human Neuronal Nitric Oxide Synthase Inhibitors.
Authors: Pensa, A.V. / Cinelli, M.A. / Li, H. / Chreifi, G. / Mukherjee, P. / Roman, L.J. / Martasek, P. / Poulos, T.L. / Silverman, R.B.
History
DepositionMay 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase, endothelial
B: Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,00411
Polymers99,4542
Non-polymers2,5509
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-118 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.530, 106.700, 156.550
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, endothelial / / endothelial nitric oxide synthase / Constitutive NOS / cNOS / EC-NOS / Endothelial NOS / eNOS / NOS ...endothelial nitric oxide synthase / Constitutive NOS / cNOS / EC-NOS / Endothelial NOS / eNOS / NOS type III / NOSIII


Mass: 49727.012 Da / Num. of mol.: 2 / Fragment: UNP residues 40-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell: endothelial / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 6 types, 250 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-XH8 / 7-(((3-(PYRIDIN-3-YL)PROPYL)AMINO)METHYL)QUINOLIN-2-


Mass: 292.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.45 Å3/Da / Density % sol: 49.8 % / Description: cubes
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20-24% PEG3350, 0.1 M cacodylate, 140-200 mM magnesium acetate, 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2015 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→64 Å / Num. obs: 49473 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.08 / Rsym value: 0.104 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 2.024 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4184 / CC1/2: 0.264 / Rpim(I) all: 1.604 / Rsym value: 2.024 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1NSE

1nse


Resolution: 2.2→63.113 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 28.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 4695 5 %random
Rwork0.1828 ---
obs0.1854 49398 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→63.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 177 241 6842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086803
X-RAY DIFFRACTIONf_angle_d1.1739291
X-RAY DIFFRACTIONf_dihedral_angle_d16.2942447
X-RAY DIFFRACTIONf_chiral_restr0.07968
X-RAY DIFFRACTIONf_plane_restr0.0051195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.42391460.39642952X-RAY DIFFRACTION98
2.225-2.25120.42441570.39882933X-RAY DIFFRACTION99
2.2512-2.27860.40361660.37442976X-RAY DIFFRACTION99
2.2786-2.30750.4141180.36562992X-RAY DIFFRACTION98
2.3075-2.33790.38271630.35132926X-RAY DIFFRACTION100
2.3379-2.36990.39821730.34322971X-RAY DIFFRACTION99
2.3699-2.40370.32731450.32422951X-RAY DIFFRACTION98
2.4037-2.43960.38441490.30082963X-RAY DIFFRACTION100
2.4396-2.47770.34541770.3142999X-RAY DIFFRACTION100
2.4777-2.51840.33521790.28252949X-RAY DIFFRACTION99
2.5184-2.56180.32121640.27842972X-RAY DIFFRACTION100
2.5618-2.60840.30671890.26732994X-RAY DIFFRACTION99
2.6084-2.65850.29311420.24382933X-RAY DIFFRACTION100
2.6585-2.71280.33291560.2333021X-RAY DIFFRACTION100
2.7128-2.77180.28851500.2362975X-RAY DIFFRACTION100
2.7718-2.83630.32671240.23293023X-RAY DIFFRACTION100
2.8363-2.90720.25331500.21843003X-RAY DIFFRACTION100
2.9072-2.98580.28191590.21283003X-RAY DIFFRACTION100
2.9858-3.07370.23311690.20172981X-RAY DIFFRACTION100
3.0737-3.17290.26421590.18842979X-RAY DIFFRACTION100
3.1729-3.28630.31400.18212993X-RAY DIFFRACTION100
3.2863-3.41780.18521680.15682991X-RAY DIFFRACTION100
3.4178-3.57340.22541600.15823003X-RAY DIFFRACTION100
3.5734-3.76180.20551550.14962964X-RAY DIFFRACTION100
3.7618-3.99740.20121460.13742949X-RAY DIFFRACTION99
3.9974-4.3060.18951570.12743006X-RAY DIFFRACTION99
4.306-4.73920.14211610.11152964X-RAY DIFFRACTION99
4.7392-5.42460.22281250.1242974X-RAY DIFFRACTION99
5.4246-6.83320.16611690.14572952X-RAY DIFFRACTION99
6.8332-63.13930.17731790.13892916X-RAY DIFFRACTION98
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)
10.9739-0.5299-0.60061.31480.60031.7450.0042-0.00460.0305-0.18440.0897-0.1676-0.06170.0932-0.07670.3663-0.07970.01220.299-0.00390.327511.09910.476931.8158
20.7627-0.41610.41431.3832-1.12282.69440.0619-0.0772-0.06790.08870.08370.023-0.0294-0.0654-0.12540.3422-0.0533-0.01280.358-0.00860.34382.71786.017867.762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 67:482)
2X-RAY DIFFRACTION2(chain B and resid 69:482)

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