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

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Basic information

Entry
Database: PDB / ID: 5vva
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-Amino-4-methylquinolin-7-yl)methyl)amino)ethyl)-2-methylbenzonitrile
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
Chem-9OJ / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase, endothelial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)102,08011
Polymers99,4542
Non-polymers2,6269
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-120 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.270, 105.950, 155.410
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, 32 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-9OJ / 4-(2-{[(2-amino-4-methylquinolin-7-yl)methyl]amino}ethyl)-2-methylbenzonitrile


Mass: 330.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N4
#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.: 23 / 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: cube
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: SSRL / Beamline: BL14-1 / Wavelength: 1.18 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2015 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.55→90 Å / Num. obs: 31268 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.077 / Rsym value: 0.085 / Net I/σ(I): 9.3
Reflection shellResolution: 2.55→2.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3658 / CC1/2: 0.276 / Rpim(I) all: 1.184 / Rsym value: 1.288 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.2.1data reduction
Aimless0.5.8data scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1NSE

1nse


Resolution: 2.55→87.542 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.08
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2889 4.91 %random
Rwork0.1823 ---
obs0.1859 31200 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→87.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 183 23 6650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016829
X-RAY DIFFRACTIONf_angle_d1.3059328
X-RAY DIFFRACTIONf_dihedral_angle_d16.082458
X-RAY DIFFRACTIONf_chiral_restr0.048970
X-RAY DIFFRACTIONf_plane_restr0.0061198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.59190.42521050.36642661X-RAY DIFFRACTION96
2.5919-2.63660.45411280.35682609X-RAY DIFFRACTION97
2.6366-2.68450.34351310.34192638X-RAY DIFFRACTION97
2.6845-2.73620.42521430.32392663X-RAY DIFFRACTION98
2.7362-2.7920.39411450.32112596X-RAY DIFFRACTION98
2.792-2.85280.37121580.30712682X-RAY DIFFRACTION99
2.8528-2.91910.33231200.28932607X-RAY DIFFRACTION99
2.9191-2.99210.31861510.26372699X-RAY DIFFRACTION99
2.9921-3.0730.32261440.25232662X-RAY DIFFRACTION99
3.073-3.16350.31921370.24242687X-RAY DIFFRACTION99
3.1635-3.26560.33381590.23612632X-RAY DIFFRACTION99
3.2656-3.38230.33331770.21452650X-RAY DIFFRACTION99
3.3823-3.51770.31581110.20492687X-RAY DIFFRACTION99
3.5177-3.67780.27091270.17492705X-RAY DIFFRACTION100
3.6778-3.87170.2471590.15872683X-RAY DIFFRACTION100
3.8717-4.11430.23061700.14342664X-RAY DIFFRACTION100
4.1143-4.43190.20481390.12462679X-RAY DIFFRACTION100
4.4319-4.87790.16451060.11412719X-RAY DIFFRACTION100
4.8779-5.58370.19831150.13132699X-RAY DIFFRACTION100
5.5837-7.03440.21421380.15982700X-RAY DIFFRACTION99
7.0344-87.59340.17591260.14552664X-RAY DIFFRACTION99
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)
10.8787-0.2699-0.70181.38130.261.6441-0.00910.0416-0.0162-0.16590.0335-0.1518-0.03870.0306-0.00930.4938-0.020.00050.466-0.00690.4911.187310.646731.6242
20.5991-0.26680.32781.0364-1.072.74720.033-0.1077-0.02410.07790.01470.0459-0.0756-0.0416-0.030.49390.004-0.01260.4853-0.01320.49422.30015.718567.2157
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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