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- PDB-5u6x: COX-1:P6 COMPLEX STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 5u6x
TitleCOX-1:P6 COMPLEX STRUCTURE
ComponentsProstaglandin G/H synthase 1
KeywordsOXIDOREDUCTASE / COX-1 / CYCLOOXYGENASE / PEROXIDASE / PROSTAGLANDIN / HEME / P6
Function / homology
Function and homology information


prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / 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 / Chem-P6A / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsCingolani, G. / Panella, A. / Perrone, M.G. / Vitale, P. / Smith, W.L. / Scilimati, A.
CitationJournal: Eur J Med Chem / Year: 2017
Title: Structural basis for selective inhibition of Cyclooxygenase-1 (COX-1) by diarylisoxazoles mofezolac and 3-(5-chlorofuran-2-yl)-5-methyl-4-phenylisoxazole (P6).
Authors: Cingolani, G. / Panella, A. / Perrone, M.G. / Vitale, P. / Di Mauro, G. / Fortuna, C.G. / Armen, R.S. / Ferorelli, S. / Smith, W.L. / Scilimati, A.
History
DepositionDec 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_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 1
B: Prostaglandin G/H synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,02715
Polymers137,8782
Non-polymers6,14913
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-6 kcal/mol
Surface area42910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.463, 181.463, 103.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Prostaglandin G/H synthase 1 / Cyclooxygenase-1 / COX-1 / Prostaglandin H2 synthase 1 / PHS 1 / Prostaglandin-endoperoxide synthase 1


Mass: 68939.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: PTGS1, COX1 / Plasmid: PFASTBAC-HTOCOX-1 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P05979, prostaglandin-endoperoxide synthase

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Sugars , 3 types, 9 molecules

#2: 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.: 4
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
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: 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.: 3
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 , 2 types, 4 molecules

#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-P6A / 3-(5-chlorofuran-2-yl)-5-methyl-4-phenyl-1,2-oxazole


Mass: 259.688 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10ClNO2

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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: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: SODIUM CITRATE, LITHIUM CHLORIDE, SODIUM AZIDE, N-OCTYL GLUCOSIDE, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. obs: 40652 / % possible obs: 97.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 64.1 Å2 / Net I/σ(I): 35.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2722: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N8Z

3n8z


Resolution: 2.93→14.991 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 2.35 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 3230 4.49 %
Rwork0.2009 --
obs0.2025 40362 88.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.93→14.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8928 0 416 0 9344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079668
X-RAY DIFFRACTIONf_angle_d0.98513196
X-RAY DIFFRACTIONf_dihedral_angle_d8.0925588
X-RAY DIFFRACTIONf_chiral_restr0.0541421
X-RAY DIFFRACTIONf_plane_restr0.0071655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9301-2.97350.36511130.35732571X-RAY DIFFRACTION76
2.9735-3.01960.31831240.33292642X-RAY DIFFRACTION78
3.0196-3.06870.33551360.32982702X-RAY DIFFRACTION80
3.0687-3.12110.4211260.32342808X-RAY DIFFRACTION83
3.1211-3.17730.31381380.29692799X-RAY DIFFRACTION84
3.1773-3.23780.35291440.29322872X-RAY DIFFRACTION85
3.2378-3.30320.32751420.29692917X-RAY DIFFRACTION87
3.3032-3.37430.3451440.27952992X-RAY DIFFRACTION89
3.3743-3.45180.25131460.25852946X-RAY DIFFRACTION87
3.4518-3.53710.35711350.24093053X-RAY DIFFRACTION90
3.5371-3.63140.22621470.23223039X-RAY DIFFRACTION91
3.6314-3.73660.23331340.21523117X-RAY DIFFRACTION91
3.7366-3.85530.26711280.20343091X-RAY DIFFRACTION91
3.8553-3.99060.20931410.1883113X-RAY DIFFRACTION91
3.9906-4.14710.24291490.18623045X-RAY DIFFRACTION91
4.1471-4.33150.2041560.1693142X-RAY DIFFRACTION93
4.3315-4.55380.20021400.15753149X-RAY DIFFRACTION93
4.5538-4.83010.17731410.15793096X-RAY DIFFRACTION93
4.8301-5.18870.21331500.15223114X-RAY DIFFRACTION92
5.1887-5.68480.24331490.16663094X-RAY DIFFRACTION92
5.6848-6.44940.23861430.18083126X-RAY DIFFRACTION92
6.4494-7.92080.14331510.17453143X-RAY DIFFRACTION93
7.9208-14.99170.16991530.1463117X-RAY DIFFRACTION92
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)
10.57810.10490.08581.53120.49360.89670.11480.05460.07990.2437-0.0209-0.35830.1864-0.4416-0.04490.3374-0.0871-0.01810.81390.0830.544544.0331146.148323.8268
20.60850.15130.13410.89290.26760.7549-0.15810.29920.0422-0.07450.1577-0.13980.1333-0.3729-0.06820.1669-0.0389-0.01691.01970.03950.485137.5602155.503916.3626
30.1014-0.1944-0.0230.40410.08440.2121-0.0287-0.1407-0.11520.14420.09570.27190.1095-0.1881-0.02450.3458-0.26570.07391.4430.06020.555122.2518144.477427.6664
40.20530.1252-0.01460.2956-0.08610.28650.1175-0.01440.08640.0518-0.16860.4465-0.099-0.5535-0.10780.11350.31430.10861.5890.0040.659817.9543174.439518.03
50.41180.1126-0.16480.75380.20131.2880.05570.00960.02770.0195-0.2459-0.0566-0.0286-0.31810.15480.21960.0897-0.0070.94510.0640.525334.6999164.185320.9508
61.76290.0468-0.09271.2068-0.69940.4070.0107-0.22640.2410.0297-0.2310.0476-0.0578-0.0920.1390.51330.3790.0961.4748-0.14920.807415.524179.803636.2309
70.3953-0.04830.02130.63580.23050.50830.0531-0.1057-0.02850.2382-0.10130.19010.123-0.51310.06110.20570.07170.10691.21510.09630.578730.6008161.771329.8976
80.38780.0058-0.13681.22420.20630.59040.04610.0415-0.0233-0.2052-0.0738-0.2848-0.1606-0.5240.0420.3030.09320.00790.91390.04280.574642.1648165.3447-11.7811
90.10190.17690.15440.420.0760.7056-0.05790.0880.0932-0.15470.01370.3421-0.1789-0.25320.02850.40940.2383-0.08691.40140.06960.595922.2417169.8631-18.0181
100.7009-0.10510.18130.17930.02680.29550.09750.0158-0.0405-0.0185-0.19630.28680.1392-0.6468-0.06970.0514-0.3256-0.09531.51420.01060.620821.8883142.0434-8.8704
111.17310.106-0.08350.7631-0.13210.02450.09990.129-0.06990.0365-0.25210.20240.156-0.31080.06240.3761-0.3177-0.10821.3713-0.11510.647118.2725138.0933-27.9604
120.1609-0.1075-0.0980.82520.22270.36290.09850.1028-0.0003-0.317-0.16910.1414-0.1005-0.43930.05440.2252-0.058-0.12451.21950.080.559631.3295153.3212-18.8411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 346 )
5X-RAY DIFFRACTION5chain 'A' and (resid 347 through 390 )
6X-RAY DIFFRACTION6chain 'A' and (resid 391 through 426 )
7X-RAY DIFFRACTION7chain 'A' and (resid 427 through 584 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 138 )
9X-RAY DIFFRACTION9chain 'B' and (resid 139 through 181 )
10X-RAY DIFFRACTION10chain 'B' and (resid 182 through 390 )
11X-RAY DIFFRACTION11chain 'B' and (resid 391 through 443 )
12X-RAY DIFFRACTION12chain 'B' and (resid 444 through 584 )

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