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- PDB-3pgh: CYCLOOXYGENASE-2 (PROSTAGLANDIN SYNTHASE-2) COMPLEXED WITH A NON-... -

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Basic information

Entry
Database: PDB / ID: 3pgh
TitleCYCLOOXYGENASE-2 (PROSTAGLANDIN SYNTHASE-2) COMPLEXED WITH A NON-SELECTIVE INHIBITOR, FLURBIPROFEN
ComponentsCYCLOOXYGENASE-2
KeywordsOXIDOREDUCTASE / PEROXIDASE / DIOXYGENASE / CYCLOOXYGENASE / NONSTEROIDAL ANTIINFLAMMATORY DRUGS / INFLAMMATION / ARTHRITIS / PROSTAGLANDIN / PROSTAGLANDIN SYNTHASE
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 / decidualization / nuclear outer membrane / 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 / cytoplasm / cytosol
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
FLURBIPROFEN / PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKurumbail, R. / Stallings, W.
Citation
Journal: Nature / Year: 1996
Title: Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents.
Authors: Kurumbail, R.G. / Stevens, A.M. / Gierse, J.K. / McDonald, J.J. / Stegeman, R.A. / Pak, J.Y. / Gildehaus, D. / Miyashiro, J.M. / Penning, T.D. / Seibert, K. / Isakson, P.C. / Stallings, W.C.
#1: Journal: Nature / Year: 1997
Title: Erratum. Structural Basis for Selective Inhibition of Cyclooxygenase-2 by Anti-Inflammatory Agents
Authors: Kurumbail, R.G. / Stevens, A.M. / Gierse, J.K. / Mcdonald, J.J. / Stegeman, R.A. / Pak, J.Y. / Gildehaus, D. / Miyashiro, J.M. / Penning, T.D. / Seibert, K. / Isakson, P.C. / Stallings, W.C.
History
DepositionDec 18, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLOOXYGENASE-2
B: CYCLOOXYGENASE-2
C: CYCLOOXYGENASE-2
D: CYCLOOXYGENASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,37224
Polymers269,2754
Non-polymers6,09720
Water00
1
A: CYCLOOXYGENASE-2
B: CYCLOOXYGENASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,68612
Polymers134,6372
Non-polymers3,04910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-26 kcal/mol
Surface area40330 Å2
MethodPISA
2
C: CYCLOOXYGENASE-2
D: CYCLOOXYGENASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,68612
Polymers134,6372
Non-polymers3,04910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-24 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.500, 133.800, 117.100
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
22
33
44
55
66
77
/ NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper:
IDCodeMatrixVector
1given(-0.9975, 0.0504, -0.0495), (0.0494, -0.0038, -0.9988), (-0.0505, -0.9987, 0.0013)93.37, 28.9991, 33.5829
2given(-0.9993, -0.0319, 0.0169), (0.0323, -0.9992, 0.0238), (0.0161, 0.0244, 0.9996)84.6166, 65.4152, 57.1417
3given(0.995, -0.0619, 0.0786), (-0.0798, -0.0171, 0.9967), (-0.0604, -0.9979, -0.022)-9.2544, 40.0367, 92.7201

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Components

#1: Protein
CYCLOOXYGENASE-2 / PROSTAGLANDIN SYNTHASE-2


Mass: 67318.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: DERMAL / Cell: FIBROBLAST / Cell line: CULTURED SF21 / Cellular location: ENDOPLASMIC RETICULUM / Cell line (production host): CULTURED SF21 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): OVARIAN TISSUE
References: UniProt: Q05769, prostaglandin-endoperoxide synthase
#2: 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.: 12
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
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-FLP / FLURBIPROFEN


Mass: 244.261 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H13FO2
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: 2.54 Å3/Da / Density % sol: 52 % / Description: PGHS-1 DIMER WAS USED AS THE SEARCH MODEL.
Crystal growpH: 8
Details: 20 MM SODIUM PHOSPHATE, 100 MM NACL, 0.6% BETA- OCTYLGLUCOSIDE, 10 MG/ML PROTEIN, 1MM INHIBITOR MIXED WITH A RESERVOIR SOLUTION CONTAINING 20-34% MONOMETHYL PEG 550, 10-240 MGCL2, 50 MM EPPS ...Details: 20 MM SODIUM PHOSPHATE, 100 MM NACL, 0.6% BETA- OCTYLGLUCOSIDE, 10 MG/ML PROTEIN, 1MM INHIBITOR MIXED WITH A RESERVOIR SOLUTION CONTAINING 20-34% MONOMETHYL PEG 550, 10-240 MGCL2, 50 MM EPPS PH 8.0 IN THE RATIO OF 1:1
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.6 %beta-OG1drop
220-34 %mPEG5501reservoir
3240 mM1reservoirMgCl2
450 mMEPPS1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: SUPPER MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 76325 / % possible obs: 77.8 % / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.32 / Rsym value: 0.425 / % possible all: 65.4
Reflection
*PLUS
Num. measured all: 2136154
Reflection shell
*PLUS
% possible obs: 65.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROSTAGLANDIN SYNTHASE-1, PDB ENTRY 1PRH

1prh


Resolution: 2.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: AS IMPLEMENTED IN X-PLOR / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.316 6027 6.36 %RANDOM
Rwork0.236 ---
obs0.236 59815 63.1 %-
Displacement parametersBiso mean: 15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17892 0 412 0 18304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.86
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINEDX-RAY DIFFRACTION1300
22X-RAY DIFFRACTION1300
33X-RAY DIFFRACTION1300
44X-RAY DIFFRACTION1300
55X-RAY DIFFRACTION1300
66X-RAY DIFFRACTION2200
77X-RAY DIFFRACTION550
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.386 486 4.2 %
Rwork0.285 4058 -
obs--38.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM_ENGH.PROTOP_ENGH.PRO
X-RAY DIFFRACTION2PARAM19X_MOD.HEMETOPH19X_MOD.HEME
X-RAY DIFFRACTION3PARAM3_MOD.CHOTOPH3.CHO
X-RAY DIFFRACTION4PARAM.FLURBIPROFENTOP.FLURBIPROFEN
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.86
LS refinement shell
*PLUS
Rfactor obs: 0.285

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