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- PDB-6vl4: Crystal Structure of mPGES-1 bound to DG-031 -

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Basic information

Entry
Database: PDB / ID: 6vl4
TitleCrystal Structure of mPGES-1 bound to DG-031
ComponentsProstaglandin E synthase
KeywordsISOMERASE / MEMBRANE PROTEIN / mPGES-1
Function / homology
Function and homology information


regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process ...regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process / nuclear envelope lumen / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / sensory perception of pain / regulation of inflammatory response / cell population proliferation / negative regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / membrane
Similarity search - Function
Microsomal glutathione S-transferase 1-like / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family
Similarity search - Domain/homology
Chem-QY1 / Prostaglandin E synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHo, J.D. / Lee, M.R. / Rauch, C.T. / Aznavour, K. / Park, J.S. / Luz, J.G. / Antonysamy, S. / Condon, B. / Maletic, M. / Zhang, A. ...Ho, J.D. / Lee, M.R. / Rauch, C.T. / Aznavour, K. / Park, J.S. / Luz, J.G. / Antonysamy, S. / Condon, B. / Maletic, M. / Zhang, A. / Hickey, M.J. / Hughes, N.E. / Chandrasekhar, S. / Sloan, A.V. / Gooding, K. / Harvey, A. / Yu, X.P. / Kahl, S.D. / Norman, B.H.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Structure-based, multi-targeted drug discovery approach to eicosanoid inhibition: Dual inhibitors of mPGES-1 and 5-lipoxygenase activating protein (FLAP).
Authors: Ho, J.D. / Lee, M.R. / Rauch, C.T. / Aznavour, K. / Park, J.S. / Luz, J.G. / Antonysamy, S. / Condon, B. / Maletic, M. / Zhang, A. / Hickey, M.J. / Hughes, N.E. / Chandrasekhar, S. / Sloan, ...Authors: Ho, J.D. / Lee, M.R. / Rauch, C.T. / Aznavour, K. / Park, J.S. / Luz, J.G. / Antonysamy, S. / Condon, B. / Maletic, M. / Zhang, A. / Hickey, M.J. / Hughes, N.E. / Chandrasekhar, S. / Sloan, A.V. / Gooding, K. / Harvey, A. / Yu, X.P. / Kahl, S.D. / Norman, B.H.
History
DepositionJan 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin E synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3665
Polymers17,3241
Non-polymers1,0424
Water1,09961
1
A: Prostaglandin E synthase
hetero molecules

A: Prostaglandin E synthase
hetero molecules

A: Prostaglandin E synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,09715
Polymers51,9713
Non-polymers3,12712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11370 Å2
ΔGint-23 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.417, 76.417, 123.784
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Prostaglandin E synthase / Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / Microsomal prostaglandin E synthase 1 / ...Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / Microsomal prostaglandin E synthase 1 / MPGES-1 / p53-induced gene 12 protein


Mass: 17323.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGES, MGST1L1, MPGES1, PGES, PIG12 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14684, prostaglandin-E synthase
#2: Chemical ChemComp-QY1 / (2R)-cyclopentyl{4-[(quinolin-2-yl)methoxy]phenyl}acetic acid


Mass: 361.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23NO3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.2 / Details: 100mM Tris HCl pH 8.2, 29% PEG 1K, 1mM DG-031

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.439
11K, H, -L20.561
ReflectionResolution: 1.4→23.19 Å / Num. obs: 52754 / % possible obs: 99.3 % / Redundancy: 5.6 % / Rsym value: 0.082 / Net I/σ(I): 10.3
Reflection shellResolution: 1.4→1.48 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 7803 / Rsym value: 0.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: mPGES

Resolution: 1.4→17.6 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.34 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.007 / ESU R Free: 0.007
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.145 2652 5 %RANDOM
Rwork0.1396 ---
obs0.1398 50099 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.66 Å2 / Biso mean: 19.196 Å2 / Biso min: 5.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2--2.51 Å20 Å2
3----5.02 Å2
Refinement stepCycle: final / Resolution: 1.4→17.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 67 61 1267
Biso mean--42.26 24.77 -
Num. residues----143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0121277
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.7011736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0065152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.09321.17651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06615194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0191511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02930
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 196 -
Rwork0.243 3738 -
all-3934 -
obs--99.97 %

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