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- PDB-2oye: Indomethacin-(R)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1 -

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Basic information

Entry
Database: PDB / ID: 2oye
TitleIndomethacin-(R)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1
ComponentsProstaglandin G/H synthase 1
KeywordsOXIDOREDUCTASE / COX / PGHS / indomethacin / NSAID / heme
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
CITRATE ANION / PROTOPORPHYRIN IX CONTAINING FE / Chem-IM8 / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHarman, C.A. / Garavito, R.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis of enantioselective inhibition of cyclooxygenase-1 by S-alpha-substituted indomethacin ethanolamides.
Authors: Harman, C.A. / Turman, M.V. / Kozak, K.R. / Marnett, L.J. / Smith, W.L. / Garavito, R.M.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
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_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _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_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.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_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999sequence There is a Met -> Leu sequence conflict at residue 92 in the Uniprot database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Prostaglandin G/H synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2689
Polymers68,8511
Non-polymers3,4178
Water48627
1
P: Prostaglandin G/H synthase 1
hetero molecules

P: Prostaglandin G/H synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,53618
Polymers137,7022
Non-polymers6,83316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_644y+1,x-1,-z-1/31
Buried area15890 Å2
ΔGint-23 kcal/mol
Surface area40620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)181.720, 181.720, 104.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11P-918-

HOH

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Components

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Protein , 1 types, 1 molecules P

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


Mass: 68851.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sheep vesicular gland / Source: (natural) Ovis aries (sheep)
References: UniProt: P05979, prostaglandin-endoperoxide synthase

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Sugars , 4 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 1
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
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 30 molecules

#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical ChemComp-IM8 / 2-[1-(4-CHLOROBENZOYL)-5-METHOXY-2-METHYL-1H-INDOL-3-YL]-N-[(1R)-1-(HYDROXYMETHYL)PROPYL]ACETAMIDE


Mass: 428.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25ClN2O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.6 Å3/Da / Density % sol: 65.84 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium Citrate, Lithium Chloride, Sodium Azide, and beta-octylglucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. all: 24207 / Num. obs: 23534 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.078 / Χ2: 1.062 / Net I/σ(I): 14.4
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.241 / Num. unique all: 1319 / Χ2: 1.113 / % possible all: 82.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MAR345data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→30 Å / FOM work R set: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 894 3.7 %RANDOM
Rwork0.245 ---
all-24142 --
obs-22532 93.3 %-
Solvent computationBsol: 22.484 Å2
Displacement parametersBiso mean: 62.963 Å2
Baniso -1Baniso -2Baniso -3
1--3.862 Å2-13.711 Å20 Å2
2---3.862 Å20 Å2
3---7.724 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.46 Å
Luzzati d res low-4.81 Å
Luzzati sigma a1.07 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 216 27 4605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.85-2.910.401480.3879991047
2.91-2.970.479550.39910511106
2.97-3.040.435390.38911241163
3.04-3.120.428440.38911741218
3.12-3.20.391500.3712001250
3.2-3.290.392530.34712351288
3.29-3.40.318490.3412661315
3.4-3.520.339480.3112821330
3.52-3.660.4490.30613241373
3.66-3.830.314600.27113151375
3.83-4.030.27580.25213441402
4.03-4.280.285490.23813381387
4.28-4.610.222610.20213531414
4.61-5.070.253550.19913581413
5.07-5.80.285690.21613701439
5.8-7.290.349570.25313991456
7.29-300.286500.2615061556
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4FE_heme.param
X-RAY DIFFRACTION5Comp8_test_trans_AM.param

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