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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


Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / hair cycle / Nicotinamide salvaging ...Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / hair cycle / Nicotinamide salvaging / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / negative regulation of synaptic transmission, dopaminergic / cellular response to lead ion / response to nematode / positive regulation of transforming growth factor beta production / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / regulation of neuroinflammatory response / positive regulation of synaptic plasticity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / response to fructose / positive regulation of smooth muscle contraction / cyclooxygenase pathway / response to fatty acid / positive regulation of fever generation / response to vitamin D / prostaglandin secretion / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / prostaglandin biosynthetic process / nuclear inner membrane / cellular response to ATP / negative regulation of smooth muscle contraction / maintenance of blood-brain barrier / positive regulation of cell migration involved in sprouting angiogenesis / bone mineralization / negative regulation of calcium ion transport / decidualization / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / response to tumor necrosis factor / brown fat cell differentiation / positive regulation of vasoconstriction / response to glucocorticoid / keratinocyte differentiation / embryo implantation / positive regulation of brown fat cell differentiation / peroxidase activity / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / memory / regulation of blood pressure / positive regulation of protein import into nucleus / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / response to estradiol / cellular response to heat / positive regulation of peptidyl-serine phosphorylation / regulation of cell population proliferation / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily ...Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(2R)-2-(3-fluoro-4-phenyl-phenyl)propanoic acid / PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin G/H synthase 2
Similarity search - Component
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.
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
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
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:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 33:583 )
211CHAIN B AND (RESSEQ 33:583 )
311CHAIN C AND (RESSEQ 33:583 )
411CHAIN D AND (RESSEQ 33:583 )

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Prostaglandin G/H synthase 2 / Cyclooxygenase / Cyclooxygenase-2 / COX-2 / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / ...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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Sugars , 2 types, 22 molecules

#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 249 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 244.261 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H13FO2 / Comment: antiinflammatory*YM
#6: Water ChemComp-HOH / water / Water


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

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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
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919044
X-RAY DIFFRACTIONf_angle_d1.23225842
X-RAY DIFFRACTIONf_dihedral_angle_d18.5257070
X-RAY DIFFRACTIONf_chiral_restr0.0822742
X-RAY DIFFRACTIONf_plane_restr0.0053296
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4474X-RAY DIFFRACTIONPOSITIONAL
12B4474X-RAY DIFFRACTIONPOSITIONAL0.041
13C4474X-RAY DIFFRACTIONPOSITIONAL0.034
14D4474X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.842-2.88620.40761140.30931999X-RAY DIFFRACTION66
2.8862-2.93350.3931240.29382299X-RAY DIFFRACTION76
2.9335-2.9840.29481070.27792367X-RAY DIFFRACTION78
2.984-3.03820.35371420.26152352X-RAY DIFFRACTION79
3.0382-3.09660.31741120.27142393X-RAY DIFFRACTION79
3.0966-3.15980.30041320.25892515X-RAY DIFFRACTION82
3.1598-3.22840.34421450.25122531X-RAY DIFFRACTION84
3.2284-3.30340.29091290.23992590X-RAY DIFFRACTION85
3.3034-3.38590.27241400.22862613X-RAY DIFFRACTION87
3.3859-3.47730.27941240.2192646X-RAY DIFFRACTION87
3.4773-3.57950.27691510.20662706X-RAY DIFFRACTION89
3.5795-3.69480.24261470.18132733X-RAY DIFFRACTION90
3.6948-3.82660.20971360.16752758X-RAY DIFFRACTION90
3.8266-3.97950.18481590.15442807X-RAY DIFFRACTION92
3.9795-4.16010.18131620.15072847X-RAY DIFFRACTION94
4.1601-4.37880.19841710.14612918X-RAY DIFFRACTION95
4.3788-4.65220.1981630.14062939X-RAY DIFFRACTION96
4.6522-5.00990.16741610.14652966X-RAY DIFFRACTION96
5.0099-5.51130.21581620.17012961X-RAY DIFFRACTION96
5.5113-6.30230.2491500.18572977X-RAY DIFFRACTION95
6.3023-7.91580.22981610.17573030X-RAY DIFFRACTION96
7.9158-29.92660.26551390.23733084X-RAY DIFFRACTION93

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