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- PDB-6n69: rat hPGDS complexed with a quinoline -

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Basic information

Entry
Database: PDB / ID: 6n69
Titlerat hPGDS complexed with a quinoline
ComponentsHematopoietic prostaglandin D synthase
KeywordsHYDROLASE / PGD2 synthase
Function / homology
Function and homology information


Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / calcium ion binding ...Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / calcium ion binding / magnesium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / quinoline-3-carbonitrile / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShewchuk, L.M. / Cleasby, A.
CitationJournal: Bioorg. Med. Chem. / Year: 2019
Title: The discovery of quinoline-3-carboxamides as hematopoietic prostaglandin D synthase (H-PGDS) inhibitors.
Authors: Deaton, D.N. / Do, Y. / Holt, J. / Jeune, M.R. / Kramer, H.F. / Larkin, A.L. / Orband-Miller, L.A. / Peckham, G.E. / Poole, C. / Price, D.J. / Schaller, L.T. / Shen, Y. / Shewchuk, L.M. / ...Authors: Deaton, D.N. / Do, Y. / Holt, J. / Jeune, M.R. / Kramer, H.F. / Larkin, A.L. / Orband-Miller, L.A. / Peckham, G.E. / Poole, C. / Price, D.J. / Schaller, L.T. / Shen, Y. / Shewchuk, L.M. / Stewart, E.L. / Stuart, J.D. / Thomson, S.A. / Ward, P. / Wilson, J.W. / Xu, T. / Guss, J.H. / Musetti, C. / Rendina, A.R. / Affleck, K. / Anders, D. / Hancock, A.P. / Hobbs, H. / Hodgson, S.T. / Hutchinson, J. / Leveridge, M.V. / Nicholls, H. / Smith, I.E.D. / Somers, D.O. / Sneddon, H.F. / Uddin, S. / Cleasby, A. / Mortenson, P.N. / Richardson, C. / Saxty, G.
History
DepositionNov 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Hematopoietic prostaglandin D synthase
B: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1356
Polymers47,2122
Non-polymers9234
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-25 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.188, 80.997, 97.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: 23606.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hpgds, Gsts, Pgds, Ptgds2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O35543, prostaglandin-D synthase, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-KDV / quinoline-3-carbonitrile


Mass: 154.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M NaF, 24.0%w/v PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→28.29 Å / Num. obs: 29490 / % possible obs: 99.3 % / Redundancy: 3.48 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2022 / Χ2: 1.2 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.429 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23145 1599 5.1 %RANDOM
Rwork0.18249 ---
obs0.18504 29490 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.109 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.62 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 2→28.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 64 297 3649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0153438
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173153
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.7544673
X-RAY DIFFRACTIONr_angle_other_deg0.4611.7257368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8585395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71821.025160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22715.162555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2841520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0213758
X-RAY DIFFRACTIONr_gen_planes_other00.021654
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0894.5251586
X-RAY DIFFRACTIONr_mcbond_other2.0884.5251587
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.875.2991852
X-RAY DIFFRACTIONr_scbond_other2.8715.3011853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.07524.7393981
X-RAY DIFFRACTIONr_long_range_B_other5.07624.6663972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 99 -
Rwork0.23 2022 -
obs--92.99 %
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)
11.0913-0.2872-0.31962.459-0.24372.22780.01980.00750.1678-0.042-0.0157-0.1433-0.17940.0486-0.00410.0834-0.0184-0.01270.0070.01040.04244.62421.2683-18.2208
21.3261-0.52060.06961.79520.29551.945-0.0304-0.0610.07190.08150.0052-0.0515-0.080.05740.02520.0513-0.0002-0.00660.01920.00650.02665.0002-3.82164.989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 199
2X-RAY DIFFRACTION2B1 - 199

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