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

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Basic information

Entry
Database: PDB / ID: 5adl
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 7-((3-(Methylamino)methyl)phenoxy)methyl)quinolin-2- amine
ComponentsENDOTHELIAL NITRIC OXIDE SYNTHASE
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric-oxide synthase activity / mitochondrion organization / arginine catabolic process / nitric oxide biosynthetic process / caveola ...cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric-oxide synthase activity / mitochondrion organization / arginine catabolic process / nitric oxide biosynthetic process / caveola / FMN binding / blood coagulation / flavin adenine dinucleotide binding / NADP binding / calmodulin binding / cytoskeleton / heme binding / Golgi apparatus / metal ion binding
Similarity search - Function
Nitric-oxide synthase, eukaryote / 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; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 3 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, N-terminal ...Nitric-oxide synthase, eukaryote / 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; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 3 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, N-terminal / 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 / Oxidoreductase NAD-binding domain / Oxidoreductase FAD/NAD(P)-binding / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / 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 / Chem-M85 / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase, endothelial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.205 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Phenyl Ether- and Aniline-Containing 2-Aminoquinolines as Potent and Selective Inhibitors of Neuronal Nitric Oxide Synthase.
Authors: Cinelli, M.A. / Li, H. / Pensa, A.V. / Kang, S. / Roman, L.J. / Martasek, P. / Poulos, T.L. / Silverman, R.B.
History
DepositionAug 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOTHELIAL NITRIC OXIDE SYNTHASE
B: ENDOTHELIAL NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,24215
Polymers99,4542
Non-polymers2,78813
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-121.5 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.958, 106.320, 157.376
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 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 , 7 types, 350 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-M85 / 7-[[3-(methylaminomethyl)phenoxy]methyl]quinolin-2-amine


Mass: 293.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19N3O
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: 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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Description: OVERALL RMERGE 0.122 RPIM 0.056 CC ONE HALF 0.998 HIGHEST RESOLUTION SHELL RMERGE 2.336 RPIM 1.123 CC ONE HALF 0.278
Crystal growpH: 6
Details: 20-22% PEG3350 0.1M CACODYLATE, 140-200 MM MG ACETATE 5 MM TCEP, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 49484 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 48.33 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.7
Reflection shellResolution: 2.21→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.7 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.205→39.176 Å / SU ML: 0.33 / σ(F): 1.02 / Phase error: 23.48 / Stereochemistry target values: ML
Details: RESIDUES 110 TO 120 IN CHAIN A AND 111 TO 120 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2059 4606 5 %
Rwork0.1604 --
obs0.1627 48832 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.205→39.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6451 0 193 337 6981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096863
X-RAY DIFFRACTIONf_angle_d1.2059368
X-RAY DIFFRACTIONf_dihedral_angle_d16.32468
X-RAY DIFFRACTIONf_chiral_restr0.072971
X-RAY DIFFRACTIONf_plane_restr0.0051202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2054-2.23040.3663890.34461887X-RAY DIFFRACTION63
2.2304-2.25660.35891480.32552899X-RAY DIFFRACTION97
2.2566-2.28420.3521450.31882963X-RAY DIFFRACTION98
2.2842-2.31310.34671450.31833003X-RAY DIFFRACTION99
2.3131-2.34350.32461550.30412947X-RAY DIFFRACTION99
2.3435-2.37560.34271550.29672954X-RAY DIFFRACTION99
2.3756-2.40950.33641700.29862983X-RAY DIFFRACTION100
2.4095-2.44550.38381560.28482931X-RAY DIFFRACTION99
2.4455-2.48370.28091650.27562954X-RAY DIFFRACTION99
2.4837-2.52440.30761810.26073001X-RAY DIFFRACTION99
2.5244-2.56790.29341710.25092937X-RAY DIFFRACTION99
2.5679-2.61460.25941700.23553001X-RAY DIFFRACTION99
2.6146-2.66490.29441540.2252955X-RAY DIFFRACTION99
2.6649-2.71930.26881550.21782975X-RAY DIFFRACTION99
2.7193-2.77840.24691480.21362958X-RAY DIFFRACTION99
2.7784-2.8430.28981200.19853013X-RAY DIFFRACTION99
2.843-2.91410.22651430.17773052X-RAY DIFFRACTION100
2.9141-2.99290.21851600.16272924X-RAY DIFFRACTION100
2.9929-3.08090.19471720.16512997X-RAY DIFFRACTION100
3.0809-3.18030.18441550.15083000X-RAY DIFFRACTION100
3.1803-3.29390.25761470.15213006X-RAY DIFFRACTION99
3.2939-3.42570.20161640.13362984X-RAY DIFFRACTION99
3.4257-3.58150.16481470.12922965X-RAY DIFFRACTION99
3.5815-3.77020.16721640.12362954X-RAY DIFFRACTION99
3.7702-4.00620.17281460.12232942X-RAY DIFFRACTION98
4.0062-4.31520.17151580.11592930X-RAY DIFFRACTION98
4.3152-4.74870.14531630.10822968X-RAY DIFFRACTION99
4.7487-5.43430.20811210.1222984X-RAY DIFFRACTION98
5.4343-6.84080.15111660.14072915X-RAY DIFFRACTION98
6.8408-39.18260.16721730.13492909X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0418-0.286-0.52261.64110.31191.7014-0.00790.00510.0154-0.2040.0718-0.2554-0.04650.0841-0.03810.1775-0.04650.02060.167-0.00570.197911.330510.391932.0364
21.1082-0.30180.26771.3966-0.87832.54130.0748-0.1105-0.07530.0990.02830.00160.0283-0.0533-0.08250.1736-0.0147-0.01120.18970.00260.18542.67825.837568.0831
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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