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- PDB-5gss: HUMAN GLUTATHIONE S-TRANSFERASE P1-1, COMPLEX WITH GLUTATHIONE -

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Basic information

Entry
Database: PDB / ID: 5gss
TitleHUMAN GLUTATHIONE S-TRANSFERASE P1-1, COMPLEX WITH GLUTATHIONE
ComponentsGLUTATHIONE S-TRANSFERASE P1-1
KeywordsTRANSFERASE / DETOXIFYING ENZYME
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 / oligodendrocyte development / Paracetamol ADME / 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 / positive regulation of superoxide anion generation / negative regulation of MAPK cascade / 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
GLUTATHIONE / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 11, 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: Version format compliance
Revision 1.3Dec 21, 2011Group: Non-polymer description
Revision 1.4Aug 9, 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)47,6937
Polymers46,4932
Non-polymers1,2005
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-9 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.336, 89.228, 68.728
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.944872, 0.144443, 0.29386), (0.144936, -0.989234, 0.02022), (0.293617, 0.023486, -0.955635)
Vector: -5.744, 20.928, 27.693)

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Components

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


Mass: 23246.570 Da / Num. of mol.: 2 / Fragment: TWO INTACT MONOMERS
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-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.56 Å3/Da / Density % sol: 52 %
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
520-34 %(w/v)ammonium sulfate1reservoir
650-80 mMdithiothreitol1reservoir
7100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 24, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 29652 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rsym value: 0.033 / Net I/σ(I): 19.2
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 6.7 / Rsym value: 0.109 / % possible all: 77
Reflection
*PLUS
% possible obs: 88 % / Num. measured all: 63592 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 77 % / Rmerge(I) obs: 0.109

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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: 1.95→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1462 4.3 %RANDOM
Rwork0.222 ---
obs0.222 28190 87.7 %-
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 75 268 3605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_d1.3
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: 1.95→2.04 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.379 191 4.5 %
Rwork0.338 3364 -
obs--84.2 %
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
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_deg1.3

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