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- PDB-3gus: Crystal strcture of human Pi class glutathione S-transferase GSTP... -

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Basic information

Entry
Database: PDB / ID: 3gus
TitleCrystal strcture of human Pi class glutathione S-transferase GSTP1-1 in complex with 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX)
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / GSTP1-1 in complex with glutathione and NBDHEX / Phosphoprotein / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / linoleic acid metabolic process / negative regulation of JUN kinase activity / nitric oxide binding / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / Paracetamol ADME / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / prostaglandin metabolic process / regulation of stress-activated MAPK cascade / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of MAPK cascade / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / negative regulation of MAP kinase activity / glutathione metabolic process / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / response to reactive oxygen species / central nervous system development / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to lipopolysaccharide / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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. ...Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Chem-N11 / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.53 Å
AuthorsFederici, L. / Lo Sterzo, C. / Di Matteo, A. / Scaloni, F. / Federici, G. / Caccuri, A.M.
CitationJournal: Cancer Res. / Year: 2009
Title: Structural basis for the binding of the anticancer compound 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol to human glutathione s-transferases
Authors: Federici, L. / Lo Sterzo, C. / Pezzola, S. / Di Matteo, A. / Scaloni, F. / Federici, G. / Caccuri, A.M.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Non-polymer description / Structure summary
Revision 1.3Nov 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 S-transferase P
B: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1899
Polymers46,4932
Non-polymers1,6967
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-32 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.587, 89.347, 69.264
Angle α, β, γ (deg.)90.00, 98.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione S-transferase P / GST class-pi / GSTP1-1


Mass: 23246.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGST-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase

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Non-polymers , 5 types, 651 molecules

#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-N11 / 6-[(7-nitro-2,1,3-benzoxadiazol-4-yl)sulfanyl]hexan-1-ol / 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol


Mass: 297.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N3O4S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8M Ammonium sulfate, 100mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 25, 2008 / Details: mirros
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.53→30 Å / Num. all: 67852 / Num. obs: 67852 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.47
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.06 / Num. unique all: 6741 / % possible all: 96.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
FFTmodel building
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb ENTRY 6GSS

6gss


Resolution: 1.53→29.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.197 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 3433 5.1 %RANDOM
Rwork0.1689 ---
obs0.17022 64412 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.967 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.34 Å2
2---0.4 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.53→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 109 644 4022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223450
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4932.0154688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7515425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62924.658146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84415558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8791516
X-RAY DIFFRACTIONr_chiral_restr0.1660.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022608
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.21715
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22363
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5181.52142
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82923353
X-RAY DIFFRACTIONr_scbond_it1.26231503
X-RAY DIFFRACTIONr_scangle_it1.8564.51331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.529→1.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 196 -
Rwork0.225 3675 -
obs--73.15 %

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