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

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Basic information

Entry
Database: PDB / ID: 5fvy
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 4-methyl-6-(2-(5-(4-methylpiperazin-1-yl)pyridin-3-yl) ethyl)pyridin-2-amine
ComponentsNITRIC OXIDE SYNTHASE, ENDOTHELIAL
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / 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 / mitochondrion organization / 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 / mitochondrion organization / negative regulation of blood pressure / nitric oxide biosynthetic process / 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 / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-W64 / Nitric oxide synthase 3
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.098 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibition by Optimization of the 2-Aminopyridine-Based Scaffold with a Pyridine Linker.
Authors: Wang, H. / Qin, Y. / Li, H. / Roman, L.J. / Martasek, P. / Poulos, T.L. / Silverman, R.B.
History
DepositionFeb 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references

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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)102,40217
Polymers99,4542
Non-polymers2,94815
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-113 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.103, 106.247, 156.183
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 / ENDOTHELIAL ...CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / ENDOTHELIAL NITRIC OXIDE SYNTHASE


Mass: 49727.012 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 8 types, 366 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-W64 / 4-methyl-6-(2-(5-(4-methylpiperazin-1-yl)pyridin-3-yl)ethyl)pyridin-2-amine


Mass: 311.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H25N5
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: 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
#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.: 351 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 100 IS FOUND AS AN ARG IN STRUCTURE BUT IS A CYS IN DATABASE

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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: 2.5 Å3/Da / Density % sol: 50.7 %
Description: OVERALL RMERGE 0.136 RPIM 0.051 CC ONE HALF 0.997 HIGHEST RESOLUTION SHELL RMERGE 1.722 RPIM 0.929 CC ONE HALF 0.324
Crystal growpH: 6
Details: 20-22% PEG3350 0.1M CACODYLATE, PH6.0 140-200 MM MG ACETATE 5 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 57071 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 36.84 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.19 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.098→87.847 Å / SU ML: 0.28 / σ(F): 0.06 / Phase error: 23.86 / Stereochemistry target values: ML
Details: RESIDUES 109 TO 119 IN CHAIN A AND 111 TO 120 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.213 5440 5 %
Rwork0.1685 --
obs0.1707 57071 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.02 Å2
Refinement stepCycle: LAST / Resolution: 2.098→87.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 203 351 6994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086840
X-RAY DIFFRACTIONf_angle_d1.169336
X-RAY DIFFRACTIONf_dihedral_angle_d16.0272466
X-RAY DIFFRACTIONf_chiral_restr0.07972
X-RAY DIFFRACTIONf_plane_restr0.0051198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0978-2.12170.31191950.30483040X-RAY DIFFRACTION88
2.1217-2.14660.37391670.30013344X-RAY DIFFRACTION96
2.1466-2.17280.30951750.29463292X-RAY DIFFRACTION96
2.1728-2.20030.36421630.29483322X-RAY DIFFRACTION96
2.2003-2.22930.3711980.28963450X-RAY DIFFRACTION100
2.2293-2.25980.37781640.32563461X-RAY DIFFRACTION99
2.2598-2.29210.28441750.25413482X-RAY DIFFRACTION100
2.2921-2.32630.3131710.25643505X-RAY DIFFRACTION100
2.3263-2.36270.28931920.22883401X-RAY DIFFRACTION100
2.3627-2.40140.27271810.22293464X-RAY DIFFRACTION100
2.4014-2.44280.30691870.21793466X-RAY DIFFRACTION100
2.4428-2.48720.26361890.21963447X-RAY DIFFRACTION100
2.4872-2.53510.26932160.20083477X-RAY DIFFRACTION100
2.5351-2.58680.25121930.19353407X-RAY DIFFRACTION100
2.5868-2.64310.251890.19153490X-RAY DIFFRACTION100
2.6431-2.70460.23721740.18433453X-RAY DIFFRACTION100
2.7046-2.77220.23841810.18313505X-RAY DIFFRACTION100
2.7722-2.84720.22281330.17873445X-RAY DIFFRACTION100
2.8472-2.9310.21091770.17643463X-RAY DIFFRACTION100
2.931-3.02560.20391940.16413483X-RAY DIFFRACTION100
3.0256-3.13370.20221880.16183445X-RAY DIFFRACTION100
3.1337-3.25920.24461800.15863496X-RAY DIFFRACTION100
3.2592-3.40750.20281890.14833458X-RAY DIFFRACTION100
3.4075-3.58720.17251710.14163447X-RAY DIFFRACTION100
3.5872-3.81190.19481830.13473466X-RAY DIFFRACTION100
3.8119-4.10620.16731730.1323476X-RAY DIFFRACTION100
4.1062-4.51940.14322010.12083449X-RAY DIFFRACTION100
4.5194-5.17340.1611550.1193462X-RAY DIFFRACTION100
5.1734-6.51760.18251910.1543477X-RAY DIFFRACTION100
6.5176-87.92440.18821950.15293421X-RAY DIFFRACTION99
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)
10.9999-0.4598-0.44841.25730.38981.76870.01420.00380.05-0.20030.0865-0.1585-0.0990.0917-0.07190.2668-0.05660.01810.1901-0.01490.23911.187210.283131.7614
20.7428-0.30020.44841.3195-0.86113.04290.0841-0.1218-0.05830.08740.05330.03170.0571-0.1563-0.09720.2128-0.0459-0.01440.2637-0.00380.23972.7125.739567.502
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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