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- PDB-1cqe: PROSTAGLANDIN H2 SYNTHASE-1 COMPLEX WITH FLURBIPROFEN -

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Basic information

Entry
Database: PDB / ID: 1cqe
TitlePROSTAGLANDIN H2 SYNTHASE-1 COMPLEX WITH FLURBIPROFEN
ComponentsPROTEIN (PROSTAGLANDIN H2 SYNTHASE-1)
KeywordsOXIDOREDUCTASE / DIOXYGENASE / PEROXIDASE
Function / homology
Function and homology information


prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin biosynthetic process / peroxidase activity / regulation of blood pressure / response to oxidative stress / neuron projection / heme binding ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin biosynthetic process / peroxidase activity / regulation of blood pressure / response to oxidative stress / neuron projection / 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 ...: / 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
FLURBIPROFEN / PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3.1 Å
AuthorsPicot, D. / Loll, P.J. / Mulichak, A.M. / Garavito, R.M.
Citation
Journal: Nature / Year: 1994
Title: The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1.
Authors: Picot, D. / Loll, P.J. / Garavito, R.M.
#1: Journal: Biochemistry / Year: 1996
Title: Synthesis and Use of Iodinated Nonsteroidal Antiinflammatory Drug Analogs as Crystallographic Probes of the Prostaglandin H2 Synthase Cyclooxygenase Active Site
Authors: Loll, P.J. / Picot, D. / Ekabo, O. / Garavito, R.M.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: The Structural Basis of Aspirin Activity Inferred from the Crystal Structure of Inactivated Prostaglandin H2 Synthase
Authors: Loll, P.J. / Picot, D. / Garavito, R.M.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: X-Ray Crystal Structure of Canine Myeloperoxidase at 3 Angstroms Resolution
Authors: Zeng, J. / Fenna, R.E.
History
DepositionJun 15, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification / _software.name
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_unobs_or_zero_occ_atoms / 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.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_unobs_or_zero_occ_atoms.label_asym_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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PROSTAGLANDIN H2 SYNTHASE-1)
B: PROTEIN (PROSTAGLANDIN H2 SYNTHASE-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,92017
Polymers133,1912
Non-polymers5,73015
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint7 kcal/mol
Surface area41250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.400, 210.300, 233.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99514, -0.06069, 0.0775), (-0.06091, -0.23886, -0.96914), (0.07733, -0.96916, 0.234)
Vector: 81.08991, 234.52885, 179.1377)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PROTEIN (PROSTAGLANDIN H2 SYNTHASE-1) / E.C.1.14.99.1 / CYCLOOXYGENASE 1 / COX-1 / PROSTAGLANDIN-ENDOPEROXIDE SYNTHASE 1


Mass: 66595.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PROTEIN IS GLYCOSYLATED AT RESIDUES ASN68, ASN144 AND ASN410
Source: (natural) Ovis aries (sheep) / Tissue: SEMINAL VESICLE
References: UniProt: P05979, prostaglandin-endoperoxide synthase

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Sugars , 2 types, 11 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.: 6
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: 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.: 5 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 134 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-FLP / FLURBIPROFEN


Mass: 244.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13FO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 73.08 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.7
Details: CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION METHOD USING 1:1 RATIO OF PROTEIN SOLUTION (10 MG/ML IN 20 MM SODIUM PHOSPHATE BUFFER PH6.7, 100-200 MM NACL, 0.6% BETA-OCTYL GLUCOPYRANOSIDE, 0. ...Details: CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION METHOD USING 1:1 RATIO OF PROTEIN SOLUTION (10 MG/ML IN 20 MM SODIUM PHOSPHATE BUFFER PH6.7, 100-200 MM NACL, 0.6% BETA-OCTYL GLUCOPYRANOSIDE, 0.1 MM FLURBIPORFEN) AND RESERVOIR OF 4-8% PEG 4000., VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
220 mMsodium phosphate1drop
3100-200 mM1dropNaCl
40.6 %(w/v)beta-octyl glucopyranoside1drop
50.1 mMflubiprofen1drop
62-4 %PEG40001drop
74-8 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorDetector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 32349 / % possible obs: 96 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 3.1→3.2 Å
Reflection
*PLUS
Num. measured all: 112745

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Processing

Software
NameVersionClassification
MADNESSdata collection
PROCORdata scaling
CCP4data reduction
MLPHAREphasing
CCP4model building
X-PLOR3.1refinement
MADNESSdata reduction
PROCORdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4665 12 %RANDOM
Rwork0.186 ---
obs0.186 40353 94.3 %-
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8923 0 360 130 9413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.1→3.2 Å / Total num. of bins used: 8
Num. reflection% reflection
Rfree481 9.2 %
Rwork4310 -
obs-92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49

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