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- PDB-2vd0: Complex structure of prostaglandin D2 synthase at 2.2A. -

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Basic information

Entry
Database: PDB / ID: 2vd0
TitleComplex structure of prostaglandin D2 synthase at 2.2A.
ComponentsGLUTATHIONE-REQUIRING 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 / response to selenium ion / response to nematode / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase ...prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / response to selenium ion / response to nematode / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / 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
Chem-D27 / GLUTATHIONE / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHohwy, M. / Spadola, L. / Lundquist, B. / von Wachenfeldt, K. / Persdotter, S. / Hawtin, P. / Dahmen, J. / Groth-Clausen, I. / Folmer, R.H.A. / Edman, K.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Novel Prostaglandin D Synthase Inhibitors Generated by Fragment-Based Drug Design.
Authors: Hohwy, M. / Spadola, L. / Lundquist, B. / Hawtin, P. / Dahmen, J. / Groth-Clausen, I. / Nilsson, E. / Persdotter, S. / Von Wachenfeldt, K. / Folmer, R.H.A. / Edman, K.
History
DepositionSep 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
B: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
C: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
D: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8259
Polymers93,4834
Non-polymers1,3415
Water5,116284
1
A: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
B: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6845
Polymers46,7422
Non-polymers9423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-23.4 kcal/mol
Surface area22510 Å2
MethodPQS
2
C: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
D: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1414
Polymers46,7422
Non-polymers3992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-32 kcal/mol
Surface area22570 Å2
MethodPQS
Unit cell
Length a, b, c (Å)123.940, 123.940, 106.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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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 / PROSTAGLANDIN D2 SYNTHASE


Mass: 23370.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CONTAIN A GLUTATHIONE CO-FACTOR. / Source: (gene. exp.) HOMO SAPIENS (human) / 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.: 3 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-D27 / 2-{[(2E)-3-(3,4-dimethoxyphenyl)prop-2-enoyl]amino}benzoic acid


Mass: 327.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17NO5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 8.4
Details: 30% PEG6000, 1% DIOXANE, 5MM DTT, 5MM GSH, 0.05 M TRISHCL PH8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 12, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.2→33 Å / Num. obs: 40755 / % possible obs: 99.8 % / Observed criterion σ(I): 1.9 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PD2

1pd2


Resolution: 2.2→32.7 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.376 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2097 5.1 %RANDOM
Rwork0.187 ---
obs0.191 38651 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 90 284 6926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9639254
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9085788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52724.217332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.492151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8291540
X-RAY DIFFRACTIONr_chiral_restr0.1040.21010
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025187
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.23190
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24668
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2421
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8181.54123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37326460
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75833167
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7634.52794
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 160 -
Rwork0.214 2830 -
obs--99.63 %

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