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- PDB-5vv6: Structure of bovine endothelial nitric oxide synthase heme domain... -

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Basic information

Entry
Database: PDB / ID: 5vv6
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 7-(((4-(Dimethylamino)phenethyl)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 / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure ...cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure / mitochondrion organization / response to hormone / caveola / blood coagulation / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to lipopolysaccharide / cytoskeleton / calmodulin binding / heme binding / Golgi apparatus / metal ion binding / nucleus / plasma membrane / cytosol
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 / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-P64 / Nitric oxide synthase 3
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 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 1.2Dec 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

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)102,37416
Polymers99,4542
Non-polymers2,92014
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-122 kcal/mol
Surface area32340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.800, 106.196, 156.672
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 , 8 types, 534 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-P64 / 7-[({2-[4-(dimethylamino)phenyl]ethyl}amino)methyl]quinolin-2-amine


Mass: 320.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N4
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: 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
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#8: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 520 / 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: BL11-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 65838 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.062 / Rsym value: 0.139 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.08 Å / Redundancy: 5.8 % / Rmerge(I) obs: 2.174 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4500 / CC1/2: 0.354 / Rpim(I) all: 0.972 / Rsym value: 2.174 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSMarch 1, 2015data reduction
Aimless0.5.8data scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→39.168 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 23.68
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 6260 5.02 %random
Rwork0.1703 ---
obs0.1727 65541 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6451 0 201 520 7172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086851
X-RAY DIFFRACTIONf_angle_d1.1899350
X-RAY DIFFRACTIONf_dihedral_angle_d15.9662463
X-RAY DIFFRACTIONf_chiral_restr0.068971
X-RAY DIFFRACTIONf_plane_restr0.0051202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9997-2.02240.36491860.33593499X-RAY DIFFRACTION89
2.0224-2.04620.3792380.33393884X-RAY DIFFRACTION97
2.0462-2.07120.35591780.33063968X-RAY DIFFRACTION99
2.0712-2.09740.3752180.31723921X-RAY DIFFRACTION99
2.0974-2.1250.32962360.30343984X-RAY DIFFRACTION99
2.125-2.15410.33021960.28983955X-RAY DIFFRACTION99
2.1541-2.18490.30022030.28183862X-RAY DIFFRACTION97
2.1849-2.21750.34732090.27334015X-RAY DIFFRACTION100
2.2175-2.25210.31342100.26143958X-RAY DIFFRACTION100
2.2521-2.28910.28972050.24853999X-RAY DIFFRACTION100
2.2891-2.32850.33151930.24473996X-RAY DIFFRACTION100
2.3285-2.37090.25782140.22363944X-RAY DIFFRACTION100
2.3709-2.41650.28462060.21494044X-RAY DIFFRACTION100
2.4165-2.46580.2932260.21773913X-RAY DIFFRACTION100
2.4658-2.51940.26232360.20453978X-RAY DIFFRACTION100
2.5194-2.5780.22462320.18663879X-RAY DIFFRACTION99
2.578-2.64240.23712050.18224010X-RAY DIFFRACTION100
2.6424-2.71390.23612070.17563990X-RAY DIFFRACTION100
2.7139-2.79370.22561980.17793915X-RAY DIFFRACTION99
2.7937-2.88380.25951720.17484042X-RAY DIFFRACTION100
2.8838-2.98690.22162150.1613938X-RAY DIFFRACTION100
2.9869-3.10640.21292230.15153990X-RAY DIFFRACTION100
3.1064-3.24770.23362000.16253985X-RAY DIFFRACTION99
3.2477-3.41890.2192040.14773978X-RAY DIFFRACTION99
3.4189-3.63290.14652080.12833958X-RAY DIFFRACTION99
3.6329-3.91320.1882150.13053950X-RAY DIFFRACTION99
3.9132-4.30650.17051940.12053927X-RAY DIFFRACTION99
4.3065-4.92870.1361980.10943993X-RAY DIFFRACTION100
4.9287-6.20560.20042060.13373989X-RAY DIFFRACTION100
6.2056-39.17550.16612290.14183906X-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)
10.978-0.4293-0.58351.20560.36291.59570.0190.01560.0221-0.15520.047-0.1606-0.03330.0929-0.05370.2203-0.03850.00950.1725-0.00730.206211.318610.226332.004
20.7013-0.31560.48391.2938-1.0172.77630.0547-0.1267-0.0750.0620.04420.02120.0307-0.1239-0.07730.1782-0.0046-0.00070.2066-0.00260.20332.58225.695567.8043
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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