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- PDB-6ztc: CRYSTAL STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE IN COMPLEX WITH FR... -

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Basic information

Entry
Database: PDB / ID: 6ztc
TitleCRYSTAL STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE IN COMPLEX WITH FRAGMENT 1A AT 1.84A RESOLUTION.
ComponentsHematopoietic prostaglandin D synthase
KeywordsISOMERASE / PROSTAGLANDIN BIOSYNTHESIS / FATTY ACID BIOSYNTHESIS / PROSTAGLANDIN D2 SYNTHASE / PGDS / ASTHMA / CYTOPLASM / LIPID SYNTHESIS
Function / homology
Function and homology information


prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior ...prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior / intracellular membrane-bounded organelle / calcium ion binding / magnesium ion binding / signal transduction / protein homodimerization activity / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Chem-QPN / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.84 Å
AuthorsSomers, D.O.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: A knowledge-based, structural-aided discovery of a novel class of 2-phenylimidazo[1,2-a]pyridine-6-carboxamide H-PGDS inhibitors.
Authors: Schulte, C.A. / Deaton, D.N. / Diaz, E. / Do, Y. / Gampe, R.T. / Guss, J.H. / Hancock, A.P. / Hobbs, H. / Hodgson, S.T. / Holt, J. / Jeune, M.R. / Kahler, K.M. / Kramer, H.F. / Le, J. / ...Authors: Schulte, C.A. / Deaton, D.N. / Diaz, E. / Do, Y. / Gampe, R.T. / Guss, J.H. / Hancock, A.P. / Hobbs, H. / Hodgson, S.T. / Holt, J. / Jeune, M.R. / Kahler, K.M. / Kramer, H.F. / Le, J. / Mortenson, P.N. / Musetti, C. / Nolte, R.T. / Orband-Miller, L.A. / Peckham, G.E. / Petrov, K.G. / Pietrak, B.L. / Poole, C. / Price, D.J. / Saxty, G. / Shillings, A. / Smalley Jr., T.L. / Somers, D.O. / Stewart, E.L. / Stuart, J.D. / Thomson, S.A.
History
DepositionJul 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hematopoietic prostaglandin D synthase
B: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,31810
Polymers46,8562
Non-polymers1,4628
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-37 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.071, 68.163, 68.517
Angle α, β, γ (deg.)90.000, 96.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hematopoietic prostaglandin D synthase / H-PGDS / GST class-sigma / Glutathione S-transferase / Glutathione-dependent PGD synthase / ...H-PGDS / GST class-sigma / Glutathione S-transferase / Glutathione-dependent PGD synthase / Glutathione-requiring prostaglandin D synthase / Prostaglandin-H2 D-isomerase


Mass: 23427.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPGDS, GSTS, PGDS, PTGDS2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60760, prostaglandin-D synthase, glutathione transferase

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Non-polymers , 5 types, 610 molecules

#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-QPN / 1-[1-(3-fluorophenyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-5-yl]propan-1-one


Mass: 273.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16FN3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: PEG6000, dioxane, TRIS-HCl, glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 21, 2010
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→21.054 Å / Num. obs: 37894 / % possible obs: 97.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.25 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.071 / Rsym value: 0.06 / Net I/av σ(I): 10.4 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.84-1.943.50.4851.61870553230.2970.570.4852.594.5
1.94-2.063.50.2852.71782851180.1750.3360.2854.395.8
2.06-2.23.50.1864.11697248700.1150.220.1866.596.9
2.2-2.383.50.135.91614145650.080.1530.138.897.8
2.38-2.63.60.0938.11541142690.0560.1090.09312.198.4
2.6-2.913.70.06711.11417038660.040.0780.06715.798.8
2.91-3.363.70.04614.91256434120.0280.0540.04622.699.1
3.36-4.113.70.03319.21084029400.020.0390.0333199.6
4.11-5.823.70.0320.4838122790.0180.0350.0333.599.8
5.82-21.0543.60.03218.1449412520.020.0380.0323397.1

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Processing

Software
NameVersionClassification
MOSFLM7.0.5data processing
SCALA3.3.15data scaling
TRUNCATE6.1data reduction
REFMACphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Coordinates determined in-house

Resolution: 1.84→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.824 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1397 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1890 5 %RANDOM
Rwork0.1637 ---
obs0.1669 35983 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 116.21 Å2 / Biso mean: 31.895 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20.35 Å2
2---1.31 Å20 Å2
3---1.93 Å2
Refinement stepCycle: final / Resolution: 1.84→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 99 602 3997
Biso mean--38.84 41.14 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123528
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.6544797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8815407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67622.41195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77215600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3441521
X-RAY DIFFRACTIONr_chiral_restr0.1090.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022776
LS refinement shellResolution: 1.84→1.887 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 126 -
Rwork0.288 2553 -
all-2679 -
obs--93.64 %

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