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- PDB-5jvz: Crystal structure of flurbiprofen bound to S121P murine COX-2 mutant -

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Basic information

Entry
Database: PDB / ID: 5jvz
TitleCrystal structure of flurbiprofen bound to S121P murine COX-2 mutant
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE / Cyclooxygenase / COX-2 / Flurbiprofen / FBP
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 / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity ...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 / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / 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 fever generation / response to selenium ion / cellular response to fluid shear stress / prostaglandin secretion / response to nematode / nuclear inner membrane / prostaglandin biosynthetic process / dioxygenase activity / bone mineralization / nuclear outer membrane / decidualization / brown fat cell differentiation / keratinocyte differentiation / positive regulation of brown fat cell differentiation / embryo implantation / peroxidase activity / regulation of blood pressure / regulation of cell population proliferation / response to oxidative stress / cellular response to hypoxia / neuron projection / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / cytosol / 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 ...: / 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
ACRYLIC ACID / PROTOPORPHYRIN IX CONTAINING CO / FLURBIPROFEN / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsMalkowski, M.G. / Orlando, B.J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Fatty Acid Binding to the Allosteric Subunit of Cyclooxygenase-2 Relieves a Tonic Inhibition of the Catalytic Subunit.
Authors: Dong, L. / Yuan, C. / Orlando, B.J. / Malkowski, M.G. / Smith, W.L.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.pdbx_aromatic_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,75619
Polymers127,1972
Non-polymers4,55917
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-1 kcal/mol
Surface area41200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.923, 131.594, 179.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Prostaglandin G/H synthase 2 / 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 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


Mass: 63598.570 Da / Num. of mol.: 2 / Mutation: S122P
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 , 4 types, 8 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 232 molecules

#4: Chemical ChemComp-FLP / FLURBIPROFEN


Mass: 244.261 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H13FO2
#6: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32CoN4O4
#8: Chemical
ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O2
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 23-34% PAA 5100, 100mM HEPES, 20mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→30 Å / Num. obs: 43042 / % possible obs: 99.8 % / Redundancy: 4.4 % / Net I/σ(I): 1.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HS5

3hs5


Resolution: 2.62→29.997 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8
RfactorNum. reflection% reflection
Rfree0.2292 2060 5.07 %
Rwork0.1816 --
obs0.184 40662 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.62→29.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9167 0 24 223 9414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039502
X-RAY DIFFRACTIONf_angle_d0.72112925
X-RAY DIFFRACTIONf_dihedral_angle_d12.6733520
X-RAY DIFFRACTIONf_chiral_restr0.0291367
X-RAY DIFFRACTIONf_plane_restr0.0031656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6174-2.67820.3429890.26061708X-RAY DIFFRACTION63
2.6782-2.74510.34531140.24722043X-RAY DIFFRACTION76
2.7451-2.81930.29151220.24122299X-RAY DIFFRACTION85
2.8193-2.90220.27371040.23812516X-RAY DIFFRACTION92
2.9022-2.99580.26391180.23842669X-RAY DIFFRACTION98
2.9958-3.10280.2691410.23172674X-RAY DIFFRACTION99
3.1028-3.22690.27011490.21552699X-RAY DIFFRACTION100
3.2269-3.37350.26861630.20852709X-RAY DIFFRACTION100
3.3735-3.55110.2431750.19132684X-RAY DIFFRACTION100
3.5511-3.77320.21771490.16482711X-RAY DIFFRACTION100
3.7732-4.06390.19641610.15042729X-RAY DIFFRACTION100
4.0639-4.47170.22791600.14222721X-RAY DIFFRACTION100
4.4717-5.1160.18451200.13562776X-RAY DIFFRACTION100
5.116-6.43510.19591350.17412799X-RAY DIFFRACTION100
6.4351-29.99880.19191600.1742865X-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)
10.6867-0.32210.17770.7157-0.4281.0907-0.0626-0.0281-0.29840.15370.2350.09130.1032-0.4526-0.14390.41670.0090.02060.58440.0440.5093119.0339163.234360.8749
21.04280.3893-0.68870.7470.09051.6936-0.25080.1946-0.081-0.0556-0.0009-0.05910.2328-0.21940.23860.4914-0.03920.02430.49760.07480.6053132.5246135.703966.1305
30.845-0.4432-0.19130.4509-0.03530.6596-0.0203-0.12450.06790.010.0525-0.07050.0050.0537-0.0230.35790.0005-0.00840.34720.00690.3778152.7236153.650361.9769
41.5294-0.1691-0.39110.69310.52070.9087-0.1546-0.23950.08810.31430.2313-0.06480.01410.1471-0.04010.51890.0420.00050.480.02330.4243163.2193148.275279.7572
50.91-0.1397-0.07630.5715-0.1390.5727-0.0786-0.21530.01190.15870.1140.04150.0008-0.0919-0.03030.39750.0317-0.0020.40290.02450.3883141.9468152.486970.8881
60.6143-0.43160.45190.7603-0.00820.69240.17290.1534-0.2866-0.1961-0.06470.22770.4535-0.1121-0.09660.6177-0.0548-0.0180.4391-0.02050.5053136.7219139.501828.7869
70.5944-0.26140.21090.8553-0.31221.16330.05770.112-0.013-0.1459-0.06760.02140.19080.12240.02090.39650.03340.01750.38420.0080.3538149.7143156.404726.9753
80.5404-0.35110.19441.07920.41641.03080.01670.04410.0896-0.09690.0158-0.0642-0.05590.0509-0.02150.35130.01720.00520.36870.03470.374137.338173.668335.0714
91.3774-0.1124-0.42311.84610.44131.20920.30150.2830.3026-0.4075-0.1518-0.0871-0.20940.3397-0.09510.49990.00810.03370.50910.06190.4078139.6126178.399314.0677
100.7815-0.1173-0.11730.5613-0.06510.87880.09710.1673-0.0996-0.2066-0.04920.00580.1628-0.0384-0.05410.44450.0101-0.01220.38510.0140.3809140.1662156.963122.3463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 33:86)
2X-RAY DIFFRACTION2(chain A and resid 87:122)
3X-RAY DIFFRACTION3(chain A and resid 123:387)
4X-RAY DIFFRACTION4(chain A and resid 388:432)
5X-RAY DIFFRACTION5(chain A and resid 433:583)
6X-RAY DIFFRACTION6(chain B and resid 33:117)
7X-RAY DIFFRACTION7(chain B and resid 118:229)
8X-RAY DIFFRACTION8(chain B and resid 230:387)
9X-RAY DIFFRACTION9(chain B and resid 388:433)
10X-RAY DIFFRACTION10(chain B and resid 434:582)

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