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- PDB-5cox: UNINHIBITED MOUSE CYCLOOXYGENASE-2 (PROSTAGLANDIN SYNTHASE-2) -

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Basic information

Entry
Database: PDB / ID: 5cox
TitleUNINHIBITED MOUSE CYCLOOXYGENASE-2 (PROSTAGLANDIN SYNTHASE-2)
ComponentsCYCLOOXYGENASE-2Prostaglandin-endoperoxide synthase 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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

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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)274,39520
Polymers269,2754
Non-polymers5,12016
Water0
1
A: CYCLOOXYGENASE-2
B: CYCLOOXYGENASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,19810
Polymers134,6372
Non-polymers2,5608
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-29 kcal/mol
Surface area41920 Å2
MethodPISA
2
C: CYCLOOXYGENASE-2
D: CYCLOOXYGENASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,19810
Polymers134,6372
Non-polymers2,5608
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-29 kcal/mol
Surface area41850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.460, 134.420, 119.900
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(-0.9998, 0.0172, -0.0137), (0.0135, -0.0116, -0.9998), (-0.0173, -0.9998, 0.0113)94.8479, 31.088, 32.2128
2given(-0.9985, -0.047, 0.0279), (0.048, -0.9982, 0.0346), (0.0262, 0.0359, 0.999)85.2601, 65.026, 57.7428
3given(0.9974, -0.0399, 0.0601), (-0.0611, -0.0238, 0.9979), (-0.0384, -0.9989, -0.0262)-10.2121, 39.6055, 93.4129

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Components

#1: Protein
CYCLOOXYGENASE-2 / Prostaglandin-endoperoxide synthase 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 / 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 / N-Acetylglucosamine


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 / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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 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 %inhibitor1drop
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: Mar 1, 1996 / Details: SUPPER MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 52156 / % possible obs: 89.2 % / Observed criterion σ(I): -1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 7.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 1.76 / Rsym value: 0.289 / % possible all: 76.8
Reflection
*PLUS
Num. measured all: 1465900
Reflection shell
*PLUS
% possible obs: 76.8 %

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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: 3→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.308 4161 7.47 %RANDOM
Rwork0.321 ---
obs0.321 41397 74.3 %-
Displacement parametersBiso mean: 11.3 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17892 0 340 0 18232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.9
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_d1.76
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: 3→3.13 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.368 296 4.3 %
Rwork0.269 2968 -
obs--47.5 %
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
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.76
LS refinement shell
*PLUS
Rfactor obs: 0.269

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