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- PDB-5fdq: Murine COX-2 S530T mutant -

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Basic information

Entry
Database: PDB / ID: 5fdq
TitleMurine COX-2 S530T mutant
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE/INHIBITOR / Cyclooxygenase / Cyxlooxygenase-2 / Monotopic / COX-2 / OXIDOREDUCTASE-INHIBITOR complex
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 / response to selenium ion / positive regulation of fever generation / prostaglandin secretion / cellular response to fluid shear stress / 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 / cellular response to hypoxia / response to oxidative stress / 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
2-[(2~{R})-2-(hydroxymethyloxy)propoxy]ethanol / ACRYLIC ACID / PROTOPORPHYRIN IX CONTAINING CO / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLucido, M.J. / Orlando, B.J. / Malkowski, M.G.
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structure of Aspirin-Acetylated Human Cyclooxygenase-2: Insight into the Formation of Products with Reversed Stereochemistry.
Authors: Lucido, M.J. / Orlando, B.J. / Vecchio, A.J. / Malkowski, M.G.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 2.1Sep 27, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 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)139,97015
Polymers135,8952
Non-polymers4,07513
Water20,6091144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-21 kcal/mol
Surface area41530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.163, 132.500, 180.488
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: 67947.414 Da / Num. of mol.: 2 / Mutation: S530T
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, 7 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.: 2
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#8: 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.: 3
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 , 4 types, 1150 molecules

#4: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#5: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2
#6: Chemical ChemComp-60A / 2-[(2~{R})-2-(hydroxymethyloxy)propoxy]ethanol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1144 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PAA-5100, HEPES(7.5), magnesium chloride, beta-octyl glucoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 112453 / % possible obs: 99.6 % / Redundancy: 3.9 % / Net I/σ(I): 10.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: truncated 3HS5

3hs5


Resolution: 1.9→19.958 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 5518 4.91 %
Rwork0.1529 --
obs0.1548 112377 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8946 0 273 1144 10363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129536
X-RAY DIFFRACTIONf_angle_d1.38212951
X-RAY DIFFRACTIONf_dihedral_angle_d14.6283505
X-RAY DIFFRACTIONf_chiral_restr0.061381
X-RAY DIFFRACTIONf_plane_restr0.0081657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.31391750.26033304X-RAY DIFFRACTION93
1.9216-1.94420.29541820.23243424X-RAY DIFFRACTION97
1.9442-1.96780.2321970.21073534X-RAY DIFFRACTION99
1.9678-1.99270.24811840.19183531X-RAY DIFFRACTION100
1.9927-2.01890.25161870.18233552X-RAY DIFFRACTION100
2.0189-2.04660.21332000.17923506X-RAY DIFFRACTION100
2.0466-2.07580.22891860.17913558X-RAY DIFFRACTION100
2.0758-2.10670.21351900.16853532X-RAY DIFFRACTION100
2.1067-2.13960.20411750.15993555X-RAY DIFFRACTION100
2.1396-2.17460.19141610.1613567X-RAY DIFFRACTION100
2.1746-2.21210.1931910.15493556X-RAY DIFFRACTION100
2.2121-2.25230.20551750.14653550X-RAY DIFFRACTION100
2.2523-2.29550.22761890.1583548X-RAY DIFFRACTION100
2.2955-2.34230.19181630.15323592X-RAY DIFFRACTION100
2.3423-2.39320.20891900.15043552X-RAY DIFFRACTION100
2.3932-2.44870.19061720.14423576X-RAY DIFFRACTION100
2.4487-2.50990.21611920.14473557X-RAY DIFFRACTION100
2.5099-2.57760.19881600.15053586X-RAY DIFFRACTION100
2.5776-2.65330.21581670.1443603X-RAY DIFFRACTION100
2.6533-2.73870.21841660.14743573X-RAY DIFFRACTION100
2.7387-2.83630.18361610.15093620X-RAY DIFFRACTION100
2.8363-2.94950.20541620.1543603X-RAY DIFFRACTION100
2.9495-3.08330.19871630.15963599X-RAY DIFFRACTION100
3.0833-3.24520.18591590.14863610X-RAY DIFFRACTION100
3.2452-3.44760.18331650.14963621X-RAY DIFFRACTION100
3.4476-3.71220.16832310.13513555X-RAY DIFFRACTION100
3.7122-4.08290.1622470.12953559X-RAY DIFFRACTION100
4.0829-4.66710.16031940.12113619X-RAY DIFFRACTION100
4.6671-5.85530.13881910.14083656X-RAY DIFFRACTION100
5.8553-19.95880.1862430.17793661X-RAY DIFFRACTION98
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)
12.66761.7464-0.20093.05940.22.66240.037-0.1863-0.1730.12850.06350.16240.0261-0.5138-0.06390.13070.02780.03390.28160.07410.2325-0.94332.57160.4282
22.93590.6636-2.44964.24550.53825.243-0.30630.3188-0.2087-0.17460.09660.3250.3351-0.36880.21110.1798-0.08170.0120.27540.0180.362212.33324.976666.4458
30.7673-0.25660.01450.6758-0.36590.7264-0.0655-0.13210.07440.17220.0489-0.0072-0.1428-0.04730.01120.15230.0096-0.00220.1161-0.01310.116823.618131.743367.2586
42.21490.57620.52711.96640.46942.99080.0151-0.09880.11930.0092-0.0157-0.1448-0.05910.1705-0.00360.07750.01510.01660.13380.02630.150747.845519.414759.7253
50.6511-0.2472-0.10730.5639-0.08690.7471-0.0368-0.1496-0.02030.11240.05440.02220.015-0.016-0.01040.1415-0.00320.0090.12420.01710.120127.460518.314568.8006
64.4781.4353-0.41633.07990.25162.7532-0.00130.0905-0.3101-0.29220.00530.13740.5539-0.1087-0.01490.3790.0056-0.02180.1263-0.02570.22729.08120.547132.5993
72.2236-0.0833-0.80693.26392.46014.3740.03870.0607-0.34070.2108-0.25710.23370.3984-0.45590.20530.2876-0.1084-0.02330.2648-0.02870.40512.657317.2125.3311
80.5739-0.25890.26950.6486-0.361.18160.05980.1021-0.0118-0.1307-0.058-0.02920.13870.0961-0.02020.1230.00980.02270.12770.00370.113530.604525.219126.613
91.14620.237-0.22671.9587-0.31932.65110.01230.08240.1666-0.05730.045-0.1377-0.1950.1562-0.02950.1244-0.00380.00490.09390.02550.16921.341450.633734.6541
100.5319-0.2768-0.16980.6424-0.04290.75980.04260.1269-0.0097-0.1428-0.00440.03330.0768-0.0518-0.03140.1212-0.0092-0.01690.14290.00910.118918.089330.924924.5681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 33:83)
2X-RAY DIFFRACTION2(chain A and resid 84:122)
3X-RAY DIFFRACTION3(chain A and resid 123:228)
4X-RAY DIFFRACTION4(chain A and resid 229:319)
5X-RAY DIFFRACTION5(chain A and resid 320:582)
6X-RAY DIFFRACTION6(chain B and resid 33:81)
7X-RAY DIFFRACTION7(chain B and resid 82:121)
8X-RAY DIFFRACTION8(chain B and resid 122:228)
9X-RAY DIFFRACTION9(chain B and resid 229:319)
10X-RAY DIFFRACTION10(chain B and resid 320:582)

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