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- PDB-8gyd: Structure of Schistosoma japonicum Glutathione S-transferase boun... -

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Basic information

Entry
Database: PDB / ID: 8gyd
TitleStructure of Schistosoma japonicum Glutathione S-transferase bound with the ligand complex of 16
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme
KeywordsTRANSFERASE / Complex
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Chem-0IH / ETHANOL / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWen, X. / Jin, R. / Hu, H. / Zhu, J. / Song, W. / Lu, X.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91953203 China
National Natural Science Foundation of China (NSFC)21877117 China
National Natural Science Foundation of China (NSFC)82173831 China
National Natural Science Foundation of China (NSFC)21907105 China
Shanghai Pujiang Program2019PJD056 China
Science and Technology Commission of Shanghai Municipality21ZR1475000 China
Shanghai Municipal Science and Technology Major Project China
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery, SAR Study of GST Inhibitors from a Novel Quinazolin-4(1 H )-one Focused DNA-Encoded Library.
Authors: Wen, X. / Zhang, M. / Duan, Z. / Suo, Y. / Lu, W. / Jin, R. / Mu, B. / Li, K. / Zhang, X. / Meng, L. / Hong, Y. / Wang, X. / Hu, H. / Zhu, J. / Song, W. / Shen, A. / Lu, X.
History
DepositionSep 22, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Sep 13, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme
B: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,76615
Polymers54,4952
Non-polymers2,27113
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: This assembly has been reported by multiple PDB structures
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-17 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.149, 64.149, 227.652
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme / GST 26 / Sj26 antigen / SjGST


Mass: 27247.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: P08515, glutathione transferase
#2: Chemical ChemComp-0IH / (2R)-2-[[2-(5-chloranylthiophen-2-yl)-4-oxidanylidene-6-[2-(1H-1,2,3,4-tetrazol-5-yl)phenyl]quinazolin-3-yl]methyl]-3-(4-chlorophenyl)propanoic acid


Mass: 603.478 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H20Cl2N6O3S
#3: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 49% Saturated ammonium sulfate, 0.3 M Sodium acetate, pH 5.6, 2% ethanol, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→55.55 Å / Num. obs: 56854 / % possible obs: 98.1 % / Redundancy: 20.6 % / CC1/2: 1 / Net I/σ(I): 36.2
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2979 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M9B

1m9b


Resolution: 1.7→16.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.102 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 2842 -RANDOM
Rwork0.1932 ---
obs0.1943 56790 98.1 %-
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.8982 Å20 Å20 Å2
2---3.8982 Å20 Å2
3---7.7964 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.7→16.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 153 247 3930
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083790HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.925114HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1309SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes617HARMONIC5
X-RAY DIFFRACTIONt_it3790HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion445SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3617SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion15.83
LS refinement shellResolution: 1.7→1.71 Å
RfactorNum. reflection% reflection
Rfree0.2892 55 -
Rwork0.2452 --
obs0.2476 1136 96.71 %
Refinement TLS params.

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)
11.473-0.5238-0.85161.39650.0273.9890.10550.1139-0.26050.1139-0.0148-0.2006-0.2605-0.2006-0.0907-0.00960.04280.04260.01430.02420.0171-2.2849-23.5957-6.7737
21.0812-0.4292-0.16462.1466-0.17513.1342-0.09060.12960.56750.1296-0.08360.34750.56750.34750.17420.17050.07130.04060.02580.00820.040610.4101-43.9147-1.9852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|305 }A1 - 216
2X-RAY DIFFRACTION1{ A|1 - A|305 }A302 - 305
3X-RAY DIFFRACTION2{ B|2 - B|304 }B2 - 216
4X-RAY DIFFRACTION2{ B|2 - B|304 }B301 - 302

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