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- PDB-5wbe: COX-1:MOFEZOLAC COMPLEX STRUCTURE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5wbe
TitleCOX-1:MOFEZOLAC COMPLEX STRUCTURE
ComponentsProstaglandin G/H synthase 1
Keywordsoxidoreductase/oxidoreductase inhibitor / COX-1 / CYCLOOXYGENASE / PEROXIDASE / PROSTAGLANDIN / HEME / MOFEZOLAC / OXIDOREDUCTASE / oxidoreductase-oxidoreductase inhibitor complex
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
Mofezolac / PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
DepositionJun 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 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_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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)144,18615
Polymers137,8782
Non-polymers6,30813
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint18 kcal/mol
Surface area42980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.925, 180.925, 104.248
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 / Production host: unidentified baculovirus
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
#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.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 42 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-63X / Mofezolac / [3,4-bis(4-methoxyphenyl)-1,2-oxazol-5-yl]acetic acid


Mass: 339.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 65.57 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.5-0.9 M LiCl, 0.7 M sodium citrate pH 6.5, 1 mM sodium azide and 0.3 %(w/v) beta-OG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 50613 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 65.5 Å2 / Rsym value: 0.087 / Net I/σ(I): 59.1
Reflection shellResolution: 2.75→2.85 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 5021 / Rsym value: 0.577 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2722: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AYL

2ayl


Resolution: 2.75→14.998 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2.35 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1843 3.96 %
Rwork0.1952 --
obs0.1965 46586 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→14.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8950 0 430 39 9419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059704
X-RAY DIFFRACTIONf_angle_d0.90513240
X-RAY DIFFRACTIONf_dihedral_angle_d8.4325612
X-RAY DIFFRACTIONf_chiral_restr0.0481421
X-RAY DIFFRACTIONf_plane_restr0.0081661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.82390.40251250.33842805X-RAY DIFFRACTION76
2.8239-2.90640.30491150.31392951X-RAY DIFFRACTION80
2.9064-2.99950.35451300.28443148X-RAY DIFFRACTION85
2.9995-3.10580.31691370.27013295X-RAY DIFFRACTION89
3.1058-3.2290.24341370.25143384X-RAY DIFFRACTION92
3.229-3.37430.29921410.24243466X-RAY DIFFRACTION94
3.3743-3.550.27031480.2173553X-RAY DIFFRACTION96
3.55-3.76910.2361490.19643612X-RAY DIFFRACTION98
3.7691-4.05480.20711480.17753645X-RAY DIFFRACTION98
4.0548-4.45310.18031550.16783684X-RAY DIFFRACTION99
4.4531-5.07550.19911530.15943688X-RAY DIFFRACTION99
5.0755-6.31420.19131470.18293737X-RAY DIFFRACTION100
6.3142-14.9980.20581580.15753775X-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)
10.526-0.3286-0.47450.40360.01760.77060.3286-0.00210.03690.384-0.1791-0.3230.60310.18610.00520.6785-0.0455-0.11250.950.08480.730136.9543133.539920.2199
21.1466-0.29-0.91991.2232-0.61471.35520.1187-0.2494-0.07980.42650.2562-0.75440.04540.4232-0.00830.41840.0147-0.10990.9927-0.07070.928650.1944161.457624.8251
30.3706-0.38480.45091.01320.07461.0902-0.04350.0138-0.17760.45420.1370.33330.4213-0.68390.01910.453-0.19410.02431.18960.07030.681323.2011144.653824.4898
40.2720.2962-0.35841.8015-0.22171.12190.11290.05840.08310.2375-0.0180.34610.1026-0.69960.01870.120.12410.05541.31060.06560.666919.1704168.181720.8909
50.8441-0.00180.72491.1450.30250.68410.0822-0.08330.28390.37160.06270.968-0.1567-0.6563-0.01610.49050.24660.10641.3990.02950.86277.235177.601220.8788
60.5987-0.32170.09582.5284-0.25952.2528-0.00220.02880.0962-0.0737-0.0768-0.0967-0.228-0.25180.00040.27440.10070.02580.9370.00910.565929.0904172.078415.85
72.3436-0.1052-0.02718.23-1.58210.3041-0.0711-0.3760.17820.6695-0.22510.0033-0.3058-0.3818-0.37720.51210.26210.24171.3969-0.10410.750113.9505178.258837.4611
81.1171-0.4650.14761.49950.91031.21670.0541-0.2602-0.06870.49280.0257-0.16290.3387-0.48480.00280.5856-0.06470.06441.13050.1010.60627.3476154.464137.153
91.3022-0.2147-0.26691.56390.33960.8529-0.0054-0.04190.09230.31970.0635-0.1449-0.2836-0.19750.00340.32030.03660.00190.9064-0.00970.591533.6509172.084920.9235
100.53580.30160.52930.32460.03380.91490.2391-0.0852-0.0782-0.2717-0.1834-0.2549-0.62130.08520.00510.66720.04860.11720.93020.09640.735436.9696179.8787-10.3803
111.1734-0.02880.90251.3049-0.58020.91110.0740.34050.0708-0.480.2245-0.739-0.02550.2941-0.00650.459-0.03330.11240.9426-0.06770.976750.1419151.7986-15.1365
120.52390.4283-0.50160.8862-0.09870.962-0.0336-0.02140.2163-0.41740.13620.2232-0.3753-0.62630.00540.47590.16690.00361.12510.07590.66623.2851169.0364-14.4859
130.3103-0.37380.27411.6067-0.18451.09020.1224-0.0202-0.0728-0.2314-0.08750.2519-0.0144-0.7809-0.00540.1417-0.1376-0.08571.30320.04120.65619.1585145.2477-11.0926
140.8435-0.1596-0.64361.12660.24310.4910.01790.3555-0.3236-0.34530.08330.97660.174-0.5869-0.00160.3973-0.316-0.13161.49980.05450.86587.2179135.839-11.0856
150.70040.495-0.01992.7112-0.41892.2543-0.0066-0.061-0.09750.0356-0.065-0.08790.2417-0.33260.0010.2788-0.1-0.03210.94530.0010.559429.0771141.3336-6.058
161.0214-0.435-0.00361.57270.11390.73390.05170.3063-0.1744-0.411-0.1103-0.02330.0499-0.5615-0.00680.5073-0.1345-0.15241.2954-0.01580.655117.8908142.4717-27.0284
170.85720.86060.29870.99630.06691.12120.15960.28650.2688-0.8066-0.0211-0.0393-0.6266-0.1973-0.00180.72340.10440.00461.08830.12630.668231.6995166.6925-27.801
181.5188-0.17770.2221.64850.16711.158-0.00010.059-0.1259-0.27690.039-0.19850.1962-0.24910.00360.3072-0.0561-0.00080.9031-0.0080.600433.5598141.1707-11.1565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 295 )
6X-RAY DIFFRACTION6chain 'A' and (resid 296 through 390 )
7X-RAY DIFFRACTION7chain 'A' and (resid 391 through 418 )
8X-RAY DIFFRACTION8chain 'A' and (resid 419 through 508 )
9X-RAY DIFFRACTION9chain 'A' and (resid 509 through 584 )
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 73 )
11X-RAY DIFFRACTION11chain 'B' and (resid 74 through 123 )
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 181 )
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 253 )
14X-RAY DIFFRACTION14chain 'B' and (resid 254 through 295 )
15X-RAY DIFFRACTION15chain 'B' and (resid 296 through 390 )
16X-RAY DIFFRACTION16chain 'B' and (resid 391 through 457 )
17X-RAY DIFFRACTION17chain 'B' and (resid 458 through 508 )
18X-RAY DIFFRACTION18chain 'B' and (resid 509 through 584 )

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