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- PDB-9mwp: Structure of human endothelial nitric oxide synthase heme domain ... -

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Basic information

Entry
Database: PDB / ID: 9mwp
TitleStructure of human endothelial nitric oxide synthase heme domain bound with N-(4-(2-((3-(furan-3-carboximidamido)benzyl)amino)ethyl)phenyl)furan-3-carboximidamide
ComponentsNitric oxide synthase 3
KeywordsOXIDOREDUCTASE / nitric oxide synthase inhibitor binding
Function / homology
Function and homology information


regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / tetrahydrobiopterin metabolic process / NOSTRIN mediated eNOS trafficking / smooth muscle hyperplasia / regulation of nervous system process / superoxide-generating NAD(P)H oxidase activity / ovulation from ovarian follicle / pulmonary valve morphogenesis ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / tetrahydrobiopterin metabolic process / NOSTRIN mediated eNOS trafficking / smooth muscle hyperplasia / regulation of nervous system process / superoxide-generating NAD(P)H oxidase activity / ovulation from ovarian follicle / pulmonary valve morphogenesis / response to fluid shear stress / negative regulation of biomineral tissue development / Nitric oxide stimulates guanylate cyclase / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / aortic valve morphogenesis / arginine binding / endocardial cushion morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / cadmium ion binding / negative regulation of calcium ion transport / negative regulation of potassium ion transport / negative regulation of platelet activation / actin monomer binding / positive regulation of blood vessel endothelial cell migration / nitric oxide mediated signal transduction / blood vessel remodeling / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / endothelial cell migration / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of blood pressure / regulation of sodium ion transport / response to hormone / nitric oxide metabolic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / homeostasis of number of cells within a tissue / removal of superoxide radicals / lung development / cell redox homeostasis / lipopolysaccharide-mediated signaling pathway / blood vessel diameter maintenance / VEGFR2 mediated vascular permeability / mitochondrion organization / negative regulation of smooth muscle cell proliferation / establishment of localization in cell / caveola / potassium ion transport / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / endocytic vesicle membrane / calcium ion transport / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to heat / scaffold protein binding / angiogenesis / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / response to lipopolysaccharide / in utero embryonic development / cytoskeleton / calmodulin binding / Extra-nuclear estrogen signaling / Golgi membrane / negative regulation of cell population proliferation / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Domain/homology
: / ACETATE ION / GADOLINIUM ATOM / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.86 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)GM131920 United States
CitationJournal: To be published
Title: A step forward for neuronal Nitric Oxide Synthase Inhibitors against Melanoma
Authors: Awasthi, A. / Li, H. / Hardy, C.D. / Poulos, T.L. / Silverman, R.B.
History
DepositionJan 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase 3
B: Nitric oxide synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,64325
Polymers98,9502
Non-polymers4,69323
Water13,151730
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-137 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.617, 109.407, 152.661
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 3 / Constitutive NOS / cNOS / EC-NOS / NOS type III / NOSIII / Nitric oxide synthase / endothelial / ...Constitutive NOS / cNOS / EC-NOS / NOS type III / NOSIII / Nitric oxide synthase / endothelial / Endothelial NOS / eNOS


Mass: 49474.949 Da / Num. of mol.: 2 / Fragment: heme domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: endothelial / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29474, nitric-oxide synthase (NADPH)

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Non-polymers , 9 types, 753 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-A1BT1 / N-[3-({[2-(4-{[(E)-(furan-3-yl)(imino)methyl]amino}phenyl)ethyl]amino}methyl)phenyl]furan-3-carboximidamide


Mass: 427.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#9: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.3 % / Description: rods
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10-12% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE 0.1M GDCL3 10% GLYCEROL, 5 MM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2024 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→47.95 Å / Num. obs: 85985 / % possible obs: 98.3 % / Redundancy: 9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.043 / Rrim(I) all: 0.13 / Net I/σ(I): 9.7 / Num. measured all: 776909
Reflection shellResolution: 1.86→1.89 Å / % possible obs: 83.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 2.614 / Num. measured all: 21004 / Num. unique obs: 3842 / CC1/2: 0.359 / Rpim(I) all: 1.206 / Rrim(I) all: 2.91 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.86→46.14 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 4171 4.98 %random
Rwork0.1793 ---
obs0.181 83777 95.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 303 730 7520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097019
X-RAY DIFFRACTIONf_angle_d1.0429549
X-RAY DIFFRACTIONf_dihedral_angle_d15.1314090
X-RAY DIFFRACTIONf_chiral_restr0.051984
X-RAY DIFFRACTIONf_plane_restr0.0061226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.88110.6972640.71491320X-RAY DIFFRACTION48
1.8811-1.90330.51541420.5112351X-RAY DIFFRACTION87
1.9033-1.92650.4594930.42571642X-RAY DIFFRACTION60
1.9265-1.95090.39991360.3942450X-RAY DIFFRACTION91
1.9509-1.97650.36341400.26512642X-RAY DIFFRACTION96
1.9765-2.00360.29741400.23412691X-RAY DIFFRACTION99
2.0036-2.03220.24081480.2042733X-RAY DIFFRACTION100
2.0322-2.06260.21811510.19442782X-RAY DIFFRACTION100
2.0626-2.09480.27351400.19322688X-RAY DIFFRACTION100
2.0948-2.12910.25191450.19092756X-RAY DIFFRACTION100
2.1291-2.16590.24621570.20932728X-RAY DIFFRACTION100
2.1659-2.20520.38371390.33752679X-RAY DIFFRACTION97
2.2052-2.24770.41851310.34642732X-RAY DIFFRACTION100
2.2477-2.29350.3391450.25452703X-RAY DIFFRACTION98
2.2935-2.34340.22061370.16752731X-RAY DIFFRACTION100
2.3434-2.39790.21361390.1592746X-RAY DIFFRACTION100
2.3979-2.45790.20021450.16072781X-RAY DIFFRACTION100
2.4579-2.52430.20421350.15572740X-RAY DIFFRACTION100
2.5243-2.59860.18591340.14992780X-RAY DIFFRACTION100
2.5986-2.68250.18981680.15522767X-RAY DIFFRACTION100
2.6825-2.77830.19461450.15352731X-RAY DIFFRACTION99
2.7783-2.88960.19421450.15732774X-RAY DIFFRACTION100
2.8896-3.0210.23311350.15862768X-RAY DIFFRACTION100
3.021-3.18030.21181270.16922812X-RAY DIFFRACTION100
3.1803-3.37950.1581710.14672764X-RAY DIFFRACTION100
3.3795-3.64030.18581340.14482816X-RAY DIFFRACTION100
3.6403-4.00650.15971400.13352796X-RAY DIFFRACTION100
4.0065-4.58580.16771640.11582822X-RAY DIFFRACTION100
4.5858-5.77580.1391440.13412858X-RAY DIFFRACTION100
5.7758-46.140.18751370.18893023X-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)
10.48510.0366-0.00080.9645-0.19651.32010.016-0.09390.09810.19970.00440.0888-0.0983-0.1349-0.02150.20020.00950.01290.2019-0.0320.198716.5933241.026131.9856
20.5540.1511-0.05161.7161-0.17450.52880.0034-0.0056-0.0183-0.1199-0.0466-0.1080.08540.01820.0410.2145-0.00080.00880.24040.00790.190329.8754213.98849.9339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 68:480)
2X-RAY DIFFRACTION2(chain B and resid 68:480)

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