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- PDB-4ee0: Crystal structure of hH-PGDS with water displacing inhibitor -

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Basic information

Entry
Database: PDB / ID: 4ee0
TitleCrystal structure of hH-PGDS with water displacing inhibitor
ComponentsHematopoietic prostaglandin D synthase
KeywordsIsomerase/Isomerase inhibitor / Inhibitor / Solvent replacement / Isomerase-Isomerase inhibitor complex
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
Chem-0O4 / L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDay, J.E. / Thorarensen, A. / Trujillo, J.I.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters.
Authors: Trujillo, J.I. / Kiefer, J.R. / Huang, W. / Day, J.E. / Moon, J. / Jerome, G.M. / Bono, C.P. / Kornmeier, C.M. / Williams, M.L. / Kuhn, C. / Rennie, G.R. / Wynn, T.A. / Carron, C.P. / Thorarensen, A.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Hematopoietic prostaglandin D synthase
B: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1817
Polymers46,7562
Non-polymers1,4265
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-19 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.612, 77.876, 52.560
Angle α, β, γ (deg.)90.00, 91.39, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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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: 23377.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTS, HPGDS, PGDS, PTGDS2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60760, prostaglandin-D synthase, glutathione transferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0O4 / 4-(isoquinolin-1-yl)-N-[2-(morpholin-4-yl)ethyl]benzamide


Mass: 361.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N3O2
#4: Chemical ChemComp-GSF / L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / GLUTATHIONE SULFINATE


Mass: 339.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growMethod: vapor diffusion / Details: vapor diffusion

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 39455 / % possible obs: 98.8 % / Rsym value: 0.066

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.73 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.541 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1305 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22323 1929 4.9 %RANDOM
Rwork0.19566 ---
obs0.19698 37441 97.87 %-
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: 29.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.58 Å2
2---0.08 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 99 307 3615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223413
X-RAY DIFFRACTIONr_bond_other_d0.0010.022304
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9894632
X-RAY DIFFRACTIONr_angle_other_deg0.82835605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26724.099161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33415568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0691520
X-RAY DIFFRACTIONr_chiral_restr0.0590.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02693
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_it0.4081.51948
X-RAY DIFFRACTIONr_mcbond_other0.0911.5773
X-RAY DIFFRACTIONr_mcangle_it0.76423165
X-RAY DIFFRACTIONr_scbond_it1.27131465
X-RAY DIFFRACTIONr_scangle_it2.0364.51467
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.739→1.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 121 -
Rwork0.294 2171 -
obs--78.71 %
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)
11.28780.02350.3221.78090.1751.85190.006-0.01170.0210.01470.0176-0.0450.04150.0753-0.02360.0158-0.00470.01360.0162-0.01340.016811.4239-0.15621.4692
21.8847-0.59050.45281.32640.0091.15130.03210.09930.0202-0.0736-0.02940.0022-0.00790.0356-0.00270.0142-0.00270.00950.0067-0.0030.0079.9707-19.6926.8058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 199
2X-RAY DIFFRACTION2B1 - 199

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