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- PDB-3rr3: Structure of (R)-flurbiprofen bound to mCOX-2 -

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Basic information

Entry
Database: PDB / ID: 3rr3
TitleStructure of (R)-flurbiprofen bound to mCOX-2
ComponentsProstaglandin G/H synthase 2Cyclooxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / flurbiprofen / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Nicotinamide salvaging / Synthesis of 15-eicosatetraenoic acid derivatives / positive regulation of platelet-derived growth factor production / cellular response to non-ionic osmotic stress / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of fibroblast growth factor production ...Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Nicotinamide salvaging / Synthesis of 15-eicosatetraenoic acid derivatives / positive regulation of platelet-derived growth factor production / cellular response to non-ionic osmotic stress / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of fibroblast growth factor production / negative regulation of synaptic transmission, dopaminergic / ovulation / positive regulation of transforming growth factor beta production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / maintenance of permeability of blood-brain barrier / negative regulation of smooth muscle contraction / positive regulation of synaptic plasticity / response to angiotensin / hair cycle / response to fructose / positive regulation of prostaglandin biosynthetic process / cellular response to lead ion / positive regulation of smooth muscle contraction / positive regulation of fever generation / response to fatty acid / regulation of neuroinflammatory response / response to vitamin D / cyclooxygenase pathway / negative regulation of calcium ion transport / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / brown fat cell differentiation / response to manganese ion / cellular response to ATP / prostaglandin biosynthetic process / bone mineralization / positive regulation of vascular endothelial growth factor production / negative regulation of cell cycle / positive regulation of cell migration involved in sprouting angiogenesis / response to lithium ion / negative regulation of blood vessel diameter / response to tumor necrosis factor / positive regulation of vasoconstriction / decidualization / positive regulation of synaptic transmission, glutamatergic / sensory perception of pain / keratinocyte differentiation / positive regulation of brown fat cell differentiation / embryo implantation / learning / positive regulation of cell death / response to cytokine / memory / peroxidase activity / response to glucocorticoid / caveola / cellular response to fluid shear stress / cellular response to UV / positive regulation of protein import into nucleus / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of blood pressure / regulation of cell population proliferation / cellular response to hypoxia / cellular response to mechanical stimulus / cellular response to heat / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-serine phosphorylation / response to estradiol / response to oxidative stress / angiogenesis / response to lipopolysaccharide / aging / inflammatory response / neuron projection / negative regulation of cell population proliferation / positive regulation of apoptotic process / endoplasmic reticulum membrane / positive regulation of cell population proliferation / heme binding / endoplasmic reticulum / negative regulation of apoptotic process / enzyme binding / protein-containing complex / protein homodimerization activity / metal ion binding / cytoplasm
Haem peroxidase domain superfamily, animal type / EGF-like domain / Haem peroxidase superfamily / Prostaglandin G/H synthase 2 / Haem peroxidase, animal-type / EGF-like domain / Animal haem peroxidase / EGF-like domain profile. / Animal heme peroxidase superfamily profile.
Prostaglandin G/H synthase 2
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.842 Å
AuthorsDuggan, K.C. / Hermanson, D.J. / Musee, J. / Prusakiewicz, J.J. / Scheib, J. / Carter, B.D. / Banerjee, S. / Oates, J.A. / Marnett, L.J.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: (R)-Profens are substrate-selective inhibitors of endocannabinoid oxygenation by COX-2.
Authors: Duggan, K.C. / Hermanson, D.J. / Musee, J. / Prusakiewicz, J.J. / Scheib, J.L. / Carter, B.D. / Banerjee, S. / Oates, J.A. / Marnett, L.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,08634
Polymers257,3494
Non-polymers8,73730
Water4,342241
1
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,04317
Polymers128,6752
Non-polymers4,36815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-19 kcal/mol
Surface area41200 Å2
MethodPISA
2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,04317
Polymers128,6752
Non-polymers4,36815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-18 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)180.615, 134.549, 122.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDSelection details
1CHAIN A AND (RESSEQ 33:583 )
2CHAIN B AND (RESSEQ 33:583 )
3CHAIN C AND (RESSEQ 33:583 )
4CHAIN D AND (RESSEQ 33:583 )

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
Prostaglandin G/H synthase 2 / Cyclooxygenase / Cyclooxygenase-2 / COX-2 / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / Macrophage activation-associated marker protein P71/73 / PES-2 / PHS II / Prostaglandin H2 synthase 2 / PGH synthase 2 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


Mass: 64337.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q05769, prostaglandin-endoperoxide synthase

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Non-polymers , 5 types, 271 molecules

#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Heme
#4: Chemical
ChemComp-FLR / (2R)-2-(3-fluoro-4-phenyl-phenyl)propanoic acid / Flurbirprofen, R-form


Mass: 244.261 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H13FO2
#5: Chemical
ChemComp-BOG / B-OCTYLGLUCOSIDE


Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Octyl glucoside / Comment: detergent *YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.56 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.842→29.925 Å / Num. all: 67187 / Num. obs: 62162 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.842→29.925 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 3131 5.04 %
Rwork0.1966 --
Obs0.199 62160 87.51 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 1.87 Å2 / ksol: 0.242 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--22.0269 Å20 Å20 Å2
2--23.1975 Å2-0 Å2
3----1.1706 Å2
Refinement stepCycle: LAST / Resolution: 2.842→29.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17896 0 588 241 18725
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.00919044
f_angle_d1.23225842
f_dihedral_angle_d18.5257070
f_chiral_restr0.0822742
f_plane_restr0.0053296
Refine LS restraints NCS

Ens-ID: 1 / Number: 4474 / Refinement-ID: X-RAY DIFFRACTION / Type: POSITIONAL

Dom-IDAuth asym-IDRms dev position (Å)
1A
2B0.041
3C0.034
4D0.04
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.842-2.88620.40761140.3093199966
2.8862-2.93350.3931240.2938229976
2.9335-2.9840.29481070.2779236778
2.984-3.03820.35371420.2615235279
3.0382-3.09660.31741120.2714239379
3.0966-3.15980.30041320.2589251582
3.1598-3.22840.34421450.2512253184
3.2284-3.30340.29091290.2399259085
3.3034-3.38590.27241400.2286261387
3.3859-3.47730.27941240.219264687
3.4773-3.57950.27691510.2066270689
3.5795-3.69480.24261470.1813273390
3.6948-3.82660.20971360.1675275890
3.8266-3.97950.18481590.1544280792
3.9795-4.16010.18131620.1507284794
4.1601-4.37880.19841710.1461291895
4.3788-4.65220.1981630.1406293996
4.6522-5.00990.16741610.1465296696
5.0099-5.51130.21581620.1701296196
5.5113-6.30230.2491500.1857297795
6.3023-7.91580.22981610.1757303096
7.9158-29.92660.26551390.2373308493

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