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- PDB-3nlt: Structure of endothelial nitric oxide synthase heme domain comple... -

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Basic information

Entry
Database: PDB / ID: 3nlt
TitleStructure of endothelial nitric oxide synthase heme domain complexed with N1-{(3'S,4'S)-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}- N2-(3'-fluorophenethyl)ethane-1,2-diamine tetrahydrochloride
ComponentsNitric oxide synthase, endothelial
KeywordsOXIDOREDUCTASE / nitric oxide synthase / heme enzyme / substrate inhibitor
Function / homology
Function and homology information


cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / : / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone ...cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / : / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / positive regulation of relaxation of smooth muscle / mitochondrion organization / caveola / response to peptide hormone / blood coagulation / NADP binding / FMN binding / flavin adenine dinucleotide 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-3XF / CACODYLIC ACID / 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: 2.74 Å
AuthorsXue, F. / Li, H. / Fang, J. / Delker, S.L. / Poulos, T.L. / Silverman, R.B.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Potent, highly selective, and orally bioavailable gem-difluorinated monocationic inhibitors of neuronal nitric oxide synthase.
Authors: Xue, F. / Li, H. / Delker, S.L. / Fang, J. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 12, 2026Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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)102,45613
Polymers99,4202
Non-polymers3,03611
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-122 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.910, 106.905, 157.024
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 NOS / eNOS / EC-NOS / NOS type III / NOSIII / Constitutive NOS / cNOS


Mass: 49710.105 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 39-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / 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 , 7 types, 71 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-3XF / 6-({(3S,4S)-4-[2-({2,2-difluoro-2-[(2R)-piperidin-2-yl]ethyl}amino)ethoxy]pyrrolidin-3-yl}methyl)-4-methylpyridin-2-amine


Mass: 397.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H33F2N5O
#6: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7AsO2
#7: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsCYS TO ARG CONFLICT IN UNP ENTRY P29473

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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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10-12% PEG 3350, 0.2M magnesium acetate, 01M sodium cacodylate, 0.005M TCEP-HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 25670 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 58.37 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 12.39
Reflection shellResolution: 2.74→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.91 / Num. unique all: 1205 / Rsym value: 0.646 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.74→36.85 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.889 / SU B: 28.688 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R Free: 0.386 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26239 1241 4.8 %RANDOM
Rwork0.1861 ---
obs0.18982 24379 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.74→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6411 0 195 60 6666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226810
X-RAY DIFFRACTIONr_angle_refined_deg1.51929302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63823.438320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.357151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4281553
X-RAY DIFFRACTIONr_chiral_restr0.0950.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215285
X-RAY DIFFRACTIONr_mcbond_it0.5551.54037
X-RAY DIFFRACTIONr_mcangle_it1.08426515
X-RAY DIFFRACTIONr_scbond_it1.80632771
X-RAY DIFFRACTIONr_scangle_it3.0344.52787
LS refinement shellResolution: 2.74→2.812 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 80 -
Rwork0.261 1612 -
obs-1612 89.38 %
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)
10.9061-0.2101-0.3941.20110.15251.8262-0.00170.0296-0.0019-0.17450.0506-0.2033-0.08350.1313-0.04880.0785-0.03610.00410.0073-0.00980.083711.11210.25631.957
20.9723-0.08030.27011.0247-0.73372.52370.0709-0.1628-0.11360.09630.04680.01340.0364-0.1362-0.11760.0443-0.0203-0.00290.0414-0.00690.09312.8635.89567.955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 482
2X-RAY DIFFRACTION2B69 - 482

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