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- PDB-10gs: HUMAN GLUTATHIONE S-TRANSFERASE P1-1, COMPLEX WITH TER117 -

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Basic information

Entry
Database: PDB / ID: 10gs
TitleHUMAN GLUTATHIONE S-TRANSFERASE P1-1, COMPLEX WITH TER117
ComponentsGLUTATHIONE S-TRANSFERASE P1-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / DETOXIFYING ENZYME / TER117 / TLK117 / RP298 / TELINTRA / EZATIOSTAT HCL / MYELODYSPLASTIC SYNDROME / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / negative regulation of smooth muscle cell chemotaxis / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / negative regulation of smooth muscle cell chemotaxis / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid / linoleic acid metabolic process / Glutathione conjugation / nitric oxide binding / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / glutathione peroxidase activity / Paracetamol ADME / oligodendrocyte development / negative regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / prostaglandin metabolic process / cellular response to glucocorticoid stimulus / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of vascular associated smooth muscle cell proliferation / glutathione transferase activity / protein serine/threonine kinase inhibitor activity / negative regulation of tumor necrosis factor production / animal organ regeneration / negative regulation of tumor necrosis factor-mediated signaling pathway / response to amino acid / toxic substance binding / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / negative regulation of MAPK cascade / positive regulation of superoxide anion generation / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / fatty acid binding / central nervous system development / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of ERK1 and ERK2 cascade / cellular response to insulin stimulus / response to estradiol / cellular response to lipopolysaccharide / response to ethanol / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol
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
Chem-VWW / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOakley, A. / Parker, M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The structures of human glutathione transferase P1-1 in complex with glutathione and various inhibitors at high resolution.
Authors: Oakley, A.J. / Bello, M.L. / Battistoni, A. / Ricci, G. / Rossjohn, J. / Villar, H.O. / Parker, M.W.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Three-Dimensional Structure of Class Pi Glutathione S-Transferase from Human Placenta in Complex with S-Hexylglutathione at 2.8 A Resolution
Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Huber, R. / Lo Bello, M. / Federici, G. / Parker, M.W.
History
DepositionAug 14, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 13, 2013Group: Structure summary
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE P1-1
B: GLUTATHIONE S-TRANSFERASE P1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8316
Polymers46,4932
Non-polymers1,3384
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-19 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.723, 90.460, 69.404
Angle α, β, γ (deg.)90.00, 98.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.945333, 0.099229, 0.310644), (0.099832, -0.994906, 0.013998), (0.310451, 0.017779, -0.950423)
Vector: -5.48795, 21.83043, 27.67516)

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE P1-1 / GSTP1-1


Mass: 23246.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: GTP_HUMAN / Organ: PLACENTA / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase
#2: Chemical ChemComp-VWW / L-gamma-glutamyl-S-benzyl-N-[(S)-carboxy(phenyl)methyl]-L-cysteinamide / TER117 / GLU-BCS-PGY


Type: peptide-like / Mass: 473.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N3O6S
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
210 mMphosphate1drop
31 mMEDTA1drop
42 mMmercaptoethanol1drop
620-34 %(w/v)ammonium sulfate1reservoir
750-80 mMdithiothreitol1reservoir
8100 mMMES1reservoir
5TER-1171drop

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 8, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 27006 / % possible obs: 83 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rsym value: 0.079 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 17.8 / Rsym value: 0.178 / % possible all: 77
Reflection
*PLUS
Num. obs: 22104 / % possible obs: 90 % / Num. measured all: 61110 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSS

1gss


Resolution: 2.2→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.214 949 4.38 %RANDOM
Rwork0.1762 ---
obs0.1762 18704 90.18 %-
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 90 169 3521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2945 116 3.75 %
Rwork0.2329 2401 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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