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

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Basic information

Entry
Database: PDB / ID: 4edz
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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0O5 / GLUTATHIONE / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Feb 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
C: Hematopoietic prostaglandin D synthase
D: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,02314
Polymers93,2434
Non-polymers2,78010
Water8,431468
1
A: Hematopoietic prostaglandin D synthase
B: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0117
Polymers46,6212
Non-polymers1,3905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-26 kcal/mol
Surface area18190 Å2
MethodPISA
2
C: Hematopoietic prostaglandin D synthase
D: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0117
Polymers46,6212
Non-polymers1,3905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-27 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.468, 124.468, 105.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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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: 23310.713 Da / Num. of mol.: 4
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-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-0O5 / 4-(3-methylisoquinolin-1-yl)-N-[2-(morpholin-4-yl)ethyl]benzamide


Mass: 375.464 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H25N3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.2 Å3/Da / Density % sol: 44.09 %
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: 2→50 Å / Num. obs: 49416 / % possible obs: 90.3 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.095 / Χ2: 1.006 / Net I/σ(I): 5.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0720.30748310.661189
2.07-2.1520.24849410.635190.9
2.15-2.2520.21449930.729191.7
2.25-2.3720.18250070.75191.5
2.37-2.522.10.15350590.779192.4
2.52-2.712.10.12449970.849191.5
2.71-2.992.10.1149470.925191
2.99-3.422.30.08650171.131191.2
3.42-4.312.40.07249221.444189.7
4.31-502.50.06947021.713184.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2233 / WRfactor Rwork: 0.1823 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8596 / SU B: 10.348 / SU ML: 0.132 / SU R Cruickshank DPI: 0.2535 / SU Rfree: 0.1952 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2482 5 %RANDOM
Rwork0.1895 ---
obs0.1919 49166 90.28 %-
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 max: 50.24 Å2 / Biso mean: 29.348 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 194 468 7206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226915
X-RAY DIFFRACTIONr_bond_other_d0.0010.024674
X-RAY DIFFRACTIONr_angle_refined_deg0.9771.989399
X-RAY DIFFRACTIONr_angle_other_deg0.808311365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8855787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16624.217332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.727151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7131540
X-RAY DIFFRACTIONr_chiral_restr0.0540.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021409
X-RAY DIFFRACTIONr_mcbond_it0.3461.53971
X-RAY DIFFRACTIONr_mcbond_other0.0681.51574
X-RAY DIFFRACTIONr_mcangle_it0.65526457
X-RAY DIFFRACTIONr_scbond_it1.03932944
X-RAY DIFFRACTIONr_scangle_it1.6844.52942
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 181 -
Rwork0.227 3397 -
all-3578 -
obs--89.2 %
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)
12.002-0.3845-0.21091.2326-0.21271.94950.04010.08840.0429-0.0228-0.0163-0.0265-0.0960.024-0.02370.0564-0.0113-0.01660.01210.01150.014424.1768.6098-27.0806
21.56670.13290.32022.19940.43732.9458-0.02760.0537-0.136-0.160.0553-0.07480.16190.1231-0.02770.02620.00330.00920.01840.0170.029125.9575-4.7281-6.9682
31.25140.1349-0.041.9342-0.0132.07780.0393-0.08980.01330.1453-0.04110.12170.0267-0.18910.00170.0096-0.01150.01050.0334-0.01630.0181-8.82526.2796-50.229
41.60140.2412-0.36731.40570.16662.3040.03930.02590.05650.057-0.0146-0.0881-0.17460.0802-0.02470.0245-0.0139-0.01080.0125-0.00490.01567.829942.5411-42.6001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 199
2X-RAY DIFFRACTION1B201
3X-RAY DIFFRACTION1A201
4X-RAY DIFFRACTION2B1 - 199
5X-RAY DIFFRACTION2B202
6X-RAY DIFFRACTION3C2 - 199
7X-RAY DIFFRACTION3C202
8X-RAY DIFFRACTION4D1 - 199
9X-RAY DIFFRACTION4D201

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