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

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Basic information

Entry
Database: PDB / ID: 5uod
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 3-[(2-Amino-4-methylquinolin-7-yl)methoxy]-5-((methylamino)methyl)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 / 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 ...cellular response to laminar fluid shear stress / 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 / NADP binding / flavin adenine dinucleotide binding / response to lipopolysaccharide / calmodulin binding / cytoskeleton / 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-8EY / 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: 2.01 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: Nitrile in the Hole: Discovery of a Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors.
Authors: Cinelli, M.A. / Li, H. / Chreifi, G. / Poulos, T.L. / Silverman, R.B.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)102,08411
Polymers99,4542
Non-polymers2,6309
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-119 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.540, 106.060, 156.650
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 / 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
Details: Residues 110 to 119 are disordered. The N-terminal residues 39 to 66 are invisible in density. Residue 100 was found as an Arg in crystal rather than a Cys
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell: endothelial / Gene: NOS3 / Plasmid: pCWori / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 6 types, 483 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
#4: Chemical ChemComp-8EY / 3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-[(methylamino)methyl]benzonitrile


Mass: 332.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N4O
#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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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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 Mg 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: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.01→80 Å / Num. obs: 62276 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.074 / Rsym value: 0.082 / Net I/σ(I): 6.6
Reflection shellResolution: 2.01→2.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4031 / CC1/2: 0.53 / Rpim(I) all: 0.767 / Rsym value: 0.863 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.01→78.325 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 23.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 5793 4.87 %random
Rwork0.1682 ---
obs0.1703 62200 96.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.01→78.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 183 474 7101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086833
X-RAY DIFFRACTIONf_angle_d1.1729332
X-RAY DIFFRACTIONf_dihedral_angle_d15.5842462
X-RAY DIFFRACTIONf_chiral_restr0.069970
X-RAY DIFFRACTIONf_plane_restr0.0051198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.03290.36941890.3393504X-RAY DIFFRACTION90
2.0329-2.05680.35771860.30423495X-RAY DIFFRACTION89
2.0568-2.08190.3492040.30433568X-RAY DIFFRACTION92
2.0819-2.10820.30941970.28893487X-RAY DIFFRACTION91
2.1082-2.1360.32341560.27433555X-RAY DIFFRACTION90
2.136-2.16520.28581870.2763626X-RAY DIFFRACTION93
2.1652-2.19620.30681910.25533613X-RAY DIFFRACTION92
2.1962-2.2290.28691720.24873660X-RAY DIFFRACTION93
2.229-2.26380.29052010.23663635X-RAY DIFFRACTION94
2.2638-2.30090.25242120.22973713X-RAY DIFFRACTION94
2.3009-2.34060.27721760.21983687X-RAY DIFFRACTION96
2.3406-2.38310.25732020.21283782X-RAY DIFFRACTION96
2.3831-2.4290.24271910.20033749X-RAY DIFFRACTION97
2.429-2.47860.26631930.19593818X-RAY DIFFRACTION97
2.4786-2.53250.24561770.18963889X-RAY DIFFRACTION98
2.5325-2.59140.25072380.18153807X-RAY DIFFRACTION98
2.5914-2.65620.25431830.17413844X-RAY DIFFRACTION99
2.6562-2.7280.22392100.16973910X-RAY DIFFRACTION99
2.728-2.80830.20511450.1713891X-RAY DIFFRACTION99
2.8083-2.89890.21681920.1743936X-RAY DIFFRACTION99
2.8989-3.00250.22362140.17533871X-RAY DIFFRACTION100
3.0025-3.12280.21031780.1663877X-RAY DIFFRACTION99
3.1228-3.26490.20911910.16863891X-RAY DIFFRACTION100
3.2649-3.4370.20262070.15043899X-RAY DIFFRACTION100
3.437-3.65240.1981850.14123941X-RAY DIFFRACTION100
3.6524-3.93440.14631830.13093895X-RAY DIFFRACTION100
3.9344-4.33030.17712230.11963886X-RAY DIFFRACTION100
4.3303-4.95680.13871780.1133912X-RAY DIFFRACTION100
4.9568-6.24460.18582330.14013884X-RAY DIFFRACTION100
6.2446-78.38450.15951990.14473896X-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)
10.6314-0.2034-0.39481.02680.221.45180.00860.01470.0229-0.19770.0427-0.1264-0.06210.0851-0.04770.2613-0.03950.00690.2248-0.00320.25111.230110.396131.9184
20.541-0.22070.29071.1435-1.02532.31510.0244-0.1328-0.05420.14280.08780.056-0.0372-0.1417-0.0910.236-0.0105-0.00980.2520.00060.24312.57845.754467.8118
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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