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- PDB-3ee2: Structure of human prostaglandin D-synthase (hGSTS1-1) in complex... -

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Basic information

Entry
Database: PDB / ID: 3ee2
TitleStructure of human prostaglandin D-synthase (hGSTS1-1) in complex with nocodazole
ComponentsGlutathione-requiring prostaglandin D synthase
KeywordsISOMERASE / H-PGDS / prostanoid production / inflamation / nocodazole / glutathione transferase sigma / Fatty acid biosynthesis / Lipid synthesis / Prostaglandin biosynthesis
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 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 / : / Glutathione S-transferase, N-terminal domain / 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 / nocodazole / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsOakley, A.J.
CitationJournal: Eur.J.Med.Chem. / Year: 2010
Title: Identification and characterisation of new inhibitors for the human hematopoietic prostaglandin D(2) synthase
Authors: Weber, J.E. / Oakley, A.J. / Christ, A.N. / Clark, A.G. / Hayes, J.D. / Hall, R. / Hume, D.A. / Board, P.G. / Smythe, M.L. / Flanagan, J.U.
History
DepositionSep 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 14, 2011Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione-requiring prostaglandin D synthase
B: Glutathione-requiring prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4035
Polymers46,7702
Non-polymers6333
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-33 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.220, 79.359, 107.547
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 Glutathione-requiring prostaglandin D synthase / Glutathione-dependent PGD synthetase / Prostaglandin-H2 D-isomerase / Hematopoietic prostaglandin D ...Glutathione-dependent PGD synthetase / Prostaglandin-H2 D-isomerase / Hematopoietic prostaglandin D synthase / H-PGDS


Mass: 23384.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGDS / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O60760, prostaglandin-D synthase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-NZO / nocodazole / methyl [6-(thiophen-2-ylcarbonyl)-1H-benzimidazol-2-yl]carbamate


Mass: 301.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11N3O3S / Comment: antineoplastic*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE AT POSITION 187 APPEARS TO BE ILE IN THIS STRUCTURE

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% (w/v) PEG 6000, 25mM MgCL2, 100mM Tris-HCl pH 7.5, 1% (w/v) dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2006
Details: LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 29738 / Num. obs: 28391 / % possible obs: 87.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Biso Wilson estimate: 25.822 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.56
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.32 / Num. unique all: 3056 / % possible all: 83.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CVD

2cvd


Resolution: 1.91→37.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.738 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R: 0.193 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23195 1435 5.1 %RANDOM
Rwork0.18337 ---
obs0.18587 26912 87.84 %-
all-29738 --
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 mean: 34.202 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.91→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 42 180 3500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223412
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9674645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28524.217166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63415586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7181520
X-RAY DIFFRACTIONr_chiral_restr0.1240.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022593
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21577
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22323
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3080.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0971.52049
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63623230
X-RAY DIFFRACTIONr_scbond_it2.69931603
X-RAY DIFFRACTIONr_scangle_it4.0614.51412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.907→1.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 102 -
Rwork0.237 1828 -
obs--82.23 %
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)
12.01560.7682-0.65292.33650.23661.40180.03090.09380.02260.0021-0.04390.143-0.0029-0.13220.013-0.17480.0149-0.0042-0.1069-0.0351-0.149722.52056.378250.5567
21.831.2067-0.56144.00780.06322.5363-0.0690.06180.0178-0.40220.01510.03110.0248-0.11470.0539-0.05850.03870.0177-0.1168-0.0244-0.130826.2596-11.958535.4168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 199
2X-RAY DIFFRACTION2B2 - 199

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