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- PDB-6ofy: Crystal Structure of Arachidonic Acid bound to V349I murine COX-2 -

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Basic information

Entry
Database: PDB / ID: 6ofy
TitleCrystal Structure of Arachidonic Acid bound to V349I murine COX-2
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE / Arachidonic Acid Cyclooxygenase Prostaglandin Endoperoxide Synthase / MEMBRANE PROTEIN
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 / hair cycle / cellular response to homocysteine / 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 / hair cycle / cellular response to homocysteine / Nicotinamide salvaging / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / 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 / positive regulation of smooth muscle contraction / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / response to fatty acid / response to fructose / positive regulation of fever generation / prostaglandin secretion / response to vitamin D / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / prostaglandin biosynthetic process / nuclear inner membrane / negative regulation of smooth muscle contraction / cellular response to ATP / positive regulation of cell migration involved in sprouting angiogenesis / maintenance of blood-brain barrier / 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 / response to glucocorticoid / keratinocyte differentiation / positive regulation of vasoconstriction / positive regulation of brown fat cell differentiation / embryo implantation / 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 / peroxidase activity / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-serine phosphorylation / response to estradiol / cellular response to heat / regulation of cell population proliferation / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / response to xenobiotic stimulus / neuron projection / positive regulation of apoptotic process / negative regulation of cell population proliferation / heme binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / 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
ARACHIDONIC ACID / 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 / molecular replacement / Resolution: 2.2 Å
AuthorsMalkowski, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115386 United States
CitationJournal: Biochemistry / Year: 2019
Title: Arg-513 and Leu-531 Are Key Residues Governing Time-Dependent Inhibition of Cyclooxygenase-2 by Aspirin and Celebrex.
Authors: Dong, L. / Anderson, A.J. / Malkowski, M.G.
History
DepositionApr 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _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_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 1.2Oct 11, 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 / pdbx_validate_chiral
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: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,20716
Polymers127,2252
Non-polymers3,98214
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, COX-2 is known to run as a dimer on a gel filtration column; detergent requirement for solubilization increases MW of peak fraction.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-26 kcal/mol
Surface area41290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.150, 135.100, 182.880
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: 63612.586 Da / Num. of mol.: 2 / Mutation: V350I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 / Plasmid: pFastBac-1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q05769, prostaglandin-endoperoxide synthase

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Sugars , 2 types, 9 molecules

#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.: 8
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
#4: 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

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Non-polymers , 4 types, 723 molecules

#3: 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.: 1 / Source method: obtained synthetically / Formula: C3H4O2
#6: Chemical ChemComp-ACD / ARACHIDONIC ACID


Mass: 304.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, sitting drop
Details: Polyacrylic Acid 5100 HEPES, pH 7.5 magnesium chloride

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.2→42.294 Å / Num. obs: 77261 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.0676 / Net I/σ(I): 6.87
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.381 / Num. unique obs: 7662 / CC1/2: 0.791 / % possible all: 99.87

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HS5 molecule A

3hs5


Resolution: 2.2→42.294 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 3762 4.87 %
Rwork0.1615 --
obs0.1636 77191 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8730 0 266 718 9714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099324
X-RAY DIFFRACTIONf_angle_d0.93112711
X-RAY DIFFRACTIONf_dihedral_angle_d4.0797428
X-RAY DIFFRACTIONf_chiral_restr0.0571359
X-RAY DIFFRACTIONf_plane_restr0.0071633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.22780.31861090.24412741X-RAY DIFFRACTION100
2.2278-2.25720.28631600.23122648X-RAY DIFFRACTION100
2.2572-2.28810.29361300.21842709X-RAY DIFFRACTION100
2.2881-2.32080.31581530.21112686X-RAY DIFFRACTION100
2.3208-2.35540.28361380.20972708X-RAY DIFFRACTION100
2.3554-2.39220.25781500.19652700X-RAY DIFFRACTION100
2.3922-2.43140.23991260.1952705X-RAY DIFFRACTION100
2.4314-2.47330.2491290.19062695X-RAY DIFFRACTION100
2.4733-2.51830.25291320.18882713X-RAY DIFFRACTION100
2.5183-2.56670.23521420.19032707X-RAY DIFFRACTION100
2.5667-2.61910.28551430.18492720X-RAY DIFFRACTION100
2.6191-2.67610.25841690.18052668X-RAY DIFFRACTION100
2.6761-2.73830.23811570.17492669X-RAY DIFFRACTION100
2.7383-2.80680.26731470.17462735X-RAY DIFFRACTION100
2.8068-2.88260.27241110.16832719X-RAY DIFFRACTION100
2.8826-2.96750.19761510.16452698X-RAY DIFFRACTION100
2.9675-3.06320.21391670.1612705X-RAY DIFFRACTION100
3.0632-3.17270.22051380.16932712X-RAY DIFFRACTION100
3.1727-3.29960.21331250.16872755X-RAY DIFFRACTION100
3.2996-3.44970.19451470.1592730X-RAY DIFFRACTION100
3.4497-3.63150.18691420.14272697X-RAY DIFFRACTION100
3.6315-3.85890.17371350.13542762X-RAY DIFFRACTION100
3.8589-4.15660.18181180.13182749X-RAY DIFFRACTION100
4.1566-4.57450.16171100.12462778X-RAY DIFFRACTION100
4.5745-5.23540.15071370.1222773X-RAY DIFFRACTION99
5.2354-6.5920.14821610.16252746X-RAY DIFFRACTION99
6.592-42.3020.15881350.17062801X-RAY DIFFRACTION96
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)
11.71220.62790.31550.43230.69981.6477-0.00340.1055-0.1466-0.22080.2711-0.5809-0.0750.6821-0.27340.2638-0.02360.10520.5443-0.08950.4142-1.2807-37.7404-63.9102
21.4697-1.2672-1.41023.22190.61132.7635-0.467-0.1498-0.51840.33350.2586-0.34120.74440.28140.18730.42950.14320.1210.4057-0.04750.6089-14.5492-63.9844-65.8979
30.96430.29260.04810.8370.51352.0073-0.09480.26820.008-0.21670.1116-0.0682-0.23560.1528-0.0040.2025-0.02320.02710.2422-0.00110.2103-23.1151-35.3363-69.7858
42.50.7893-0.06451.11190.11761.5854-0.06140.37190.0746-0.02920.03320.30180.1226-0.36720.03810.1809-0.03470.02420.3013-0.05470.2674-46.2147-45.6883-60.4368
51.10230.2842-0.48081.10740.19161.8445-0.120.1981-0.2133-0.01270.0763-0.1060.3751-0.01110.05660.20720.00110.02480.1835-0.05660.2621-28.6542-53.2039-59.5906
64.71030.3151-0.3082.4176-2.34442.2818-0.23480.6290.0085-0.47630.21140.38660.3109-0.70790.04440.331-0.1287-0.01060.6563-0.07550.2906-46.6563-50.0663-80.5519
70.94480.2861-0.25721.08960.15541.4607-0.10250.3231-0.135-0.21130.1027-0.12140.07610.10830.00820.2515-0.02590.04160.3091-0.06740.2343-23.4641-45.9488-72.2609
81.78970.86760.59921.44270.58421.58770.076-0.157-0.48510.2375-0.0042-0.34440.75390.2007-0.08140.61680.1091-0.01070.3040.06190.4616-20.159-61.0214-29.262
92.92260.97861.19090.61540.08440.97150.0440.191-0.54180.13240.081-0.29740.4060.277-0.11680.33220.09480.01050.2616-0.03640.3401-18.2315-49.3307-36.2414
100.54770.21410.42230.64730.61741.77120.1101-0.2069-0.06390.2805-0.10270.03910.4245-0.1456-0.00810.2706-0.02270.01610.23780.01560.2305-30.4076-41.6372-22.4228
110.95580.198-0.12231.78590.1671.81510.0307-0.07330.10280.0510.0716-0.0351-0.14940.1354-0.08930.1474-0.0260.01240.1615-0.02890.2108-19.4836-25.8915-35.2055
122.9455-0.3848-2.69764.6853-1.38963.24910.1842-0.43960.39630.42180.07750.0335-0.31040.242-0.25050.3034-0.06120.02680.3525-0.10950.2641-19.9483-17.4789-14.9728
131.04290.2741-0.05720.91260.34721.5520.0547-0.2458-0.16240.26920.0131-0.11650.36690.1069-0.05630.28750.0282-0.04180.24060.00990.2291-20.3355-41.1679-22.7747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 209 )
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 320 )
5X-RAY DIFFRACTION5chain 'A' and (resid 321 through 391 )
6X-RAY DIFFRACTION6chain 'A' and (resid 392 through 429 )
7X-RAY DIFFRACTION7chain 'A' and (resid 430 through 583 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 106 )
9X-RAY DIFFRACTION9chain 'B' and (resid 107 through 139 )
10X-RAY DIFFRACTION10chain 'B' and (resid 140 through 209 )
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 391 )
12X-RAY DIFFRACTION12chain 'B' and (resid 392 through 429 )
13X-RAY DIFFRACTION13chain 'B' and (resid 430 through 583 )

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