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- PDB-1aqv: GLUTATHIONE S-TRANSFERASE IN COMPLEX WITH P-BROMOBENZYLGLUTATHIONE -

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Basic information

Entry
Database: PDB / ID: 1aqv
TitleGLUTATHIONE S-TRANSFERASE IN COMPLEX WITH P-BROMOBENZYLGLUTATHIONE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / CLASS PI
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
Chem-0HG / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPrade, L. / Huber, R. / Manoharan, T.H. / Fahl, W.E. / Reuter, W.
CitationJournal: Structure / Year: 1997
Title: Structures of class pi glutathione S-transferase from human placenta in complex with substrate, transition-state analogue and inhibitor.
Authors: Prade, L. / Huber, R. / Manoharan, T.H. / Fahl, W.E. / Reuter, W.
History
DepositionAug 1, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Feb 7, 2024Group: 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 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8386
Polymers46,4932
Non-polymers1,3454
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.660, 90.070, 69.570
Angle α, β, γ (deg.)90.00, 99.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.934172, -0.100241, 0.342452), (-0.099906, -0.994822, -0.018668), (0.34255, -0.016774, -0.93935)
Vector: -4.81902, 1.8728, 27.57735)

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE / GST


Mass: 23246.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOSOL / Gene: GTP_HUMAN / Organ: PLACENTA / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase
#2: Chemical ChemComp-0HG / N-[(4S)-4-ammonio-4-carboxybutanoyl]-S-(4-bromobenzyl)-L-cysteinylglycine / S-(p-bromobenzyl)-glutathione


Type: peptide-like / Mass: 477.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23BrN3O6S
#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.: 247 / 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: 57 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113.3 mg/mlprotein1drop0.004ml
210 %PEG80001drop
333.3 mMMes-NaOH1drop
45 mMligand1drop
530 %PEG80001reservoir
6100 mMMes=NaOH1reservoir
7200 mM1reservoirNaAc
866.7 mM1dropNaAc

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 28, 1996
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→12.8 Å / Num. obs: 34247 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 2.67 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.08 / Net I/σ(I): 15
Reflection shellResolution: 1.939→1.99 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3 / Rsym value: 0.242 / % possible all: 88
Reflection
*PLUS
Num. measured all: 91365
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.5refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→7 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2955 5 %RANDOM
Rwork0.194 ---
obs0.194 33587 93 %-
Displacement parametersBiso mean: 14.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.94→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 80 247 3603
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.666
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.04
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it2.52.5
LS refinement shellResolution: 1.94→1.96 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.2842 25 3 %
Rwork0.2477 415 -
obs--53 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR3.5 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.25
LS refinement shell
*PLUS
Rfactor obs: 0.2477

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