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- PDB-5vv9: Structure of bovine endothelial nitric oxide synthase heme domain... -

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Basic information

Entry
Database: PDB / ID: 5vv9
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-Amino-4-methylquinolin-7-yl)methyl)amino)ethyl)benzonitrile
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 mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of blood pressure / response to hormone ...cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of blood pressure / response to hormone / nitric oxide biosynthetic process / mitochondrion organization / 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, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 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, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 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
Chem-9OG / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 3
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)102,05211
Polymers99,4542
Non-polymers2,5989
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-117 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.245, 106.127, 155.832
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 (domestic 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 , 5 types, 9 molecules

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


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


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#4: Chemical ChemComp-9OG / 4-(2-{[(2-amino-4-methylquinolin-7-yl)methyl]amino}ethyl)benzonitrile


Mass: 316.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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

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Details

Has protein modificationY

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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: 2.5→50 Å / Num. obs: 33655 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.074 / Rsym value: 0.132 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.33 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3703 / CC1/2: 0.268 / Rpim(I) all: 1.308 / Rsym value: 2.33 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSoct. 15, 2015data reduction
Aimless0.5.8data scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1NSE

1nse


Resolution: 2.5→38.916 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 33.48
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3077 4.96 %random
Rwork0.1857 ---
obs0.1892 32952 97.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 181 0 6625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016827
X-RAY DIFFRACTIONf_angle_d1.3379324
X-RAY DIFFRACTIONf_dihedral_angle_d16.9422458
X-RAY DIFFRACTIONf_chiral_restr0.049970
X-RAY DIFFRACTIONf_plane_restr0.0061198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.5390.5061850.43431908X-RAY DIFFRACTION70
2.539-2.58060.43371340.40912542X-RAY DIFFRACTION92
2.5806-2.62510.41011380.38392613X-RAY DIFFRACTION95
2.6251-2.67280.37271260.39132629X-RAY DIFFRACTION97
2.6728-2.72420.40371490.36992767X-RAY DIFFRACTION99
2.7242-2.77980.43651350.3622663X-RAY DIFFRACTION99
2.7798-2.84020.41511430.35362728X-RAY DIFFRACTION99
2.8402-2.90630.39161460.33892733X-RAY DIFFRACTION100
2.9063-2.97890.37881380.30142727X-RAY DIFFRACTION100
2.9789-3.05940.38261480.27782757X-RAY DIFFRACTION100
3.0594-3.14940.35111470.26432731X-RAY DIFFRACTION100
3.1494-3.2510.30981460.24812712X-RAY DIFFRACTION100
3.251-3.36720.3211430.22732764X-RAY DIFFRACTION100
3.3672-3.50190.27911430.18432728X-RAY DIFFRACTION100
3.5019-3.66120.18291460.15992734X-RAY DIFFRACTION100
3.6612-3.8540.2641450.15742742X-RAY DIFFRACTION100
3.854-4.09530.24211460.14662764X-RAY DIFFRACTION100
4.0953-4.41110.20511420.12562733X-RAY DIFFRACTION100
4.4111-4.85420.18711440.11072725X-RAY DIFFRACTION100
4.8542-5.55490.19961400.12782740X-RAY DIFFRACTION100
5.5549-6.99190.17021500.14372732X-RAY DIFFRACTION100
6.9919-38.92060.20861430.12862732X-RAY DIFFRACTION100
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)
10.9226-0.3941-0.61991.46140.10911.87020.01210.042-0.007-0.21560.0215-0.1573-0.03680.0577-0.02470.5526-0.0505-0.00120.4845-0.01640.511311.185610.591731.7614
20.797-0.34760.37631.2133-1.01592.5962-0.0095-0.0693-0.02680.10030.05330.041-0.1075-0.0684-0.03110.578-0.016-0.00040.50170.00370.50042.33425.710467.4251
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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