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- PDB-3n9j: Structure of human Glutathione Transferase Pi class in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3n9j
TitleStructure of human Glutathione Transferase Pi class in complex with Ethacraplatin
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE / GLUTATHIONE / DETOXIFICATION / ETHACRYNIC ACID / CISPLATIN / PRODRUG / ETHACRAPLATIN / PLATINUM
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 / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / Paracetamol ADME / JUN kinase binding / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / negative regulation of MAPK cascade / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / 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 canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / glutathione metabolic process / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / response to reactive oxygen species / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / vesicle / cellular response to lipopolysaccharide / 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 / 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, 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 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ETHACRYNIC ACID / : / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Difference Fourier / Resolution: 1.85 Å
AuthorsParker, L.J. / Parker, M.W.
CitationJournal: To be Published
Title: Studies of glutathione transferase P1-1 bound to a platinum(IV)-based anticancer compound reveal the molecular basis of its activation.
Authors: Parker, L.J. / Italiano, L.C. / Morton, C.J. / Hancock, N.C. / Ascher, D.B. / Aitken, J.B. / Harris, H.H. / Campomanes, P. / Rothlisberger, U. / De Luca, A. / Lo Bello, M. / Ang, W.H. / ...Authors: Parker, L.J. / Italiano, L.C. / Morton, C.J. / Hancock, N.C. / Ascher, D.B. / Aitken, J.B. / Harris, H.H. / Campomanes, P. / Rothlisberger, U. / De Luca, A. / Lo Bello, M. / Ang, W.H. / Dyson, P.J. / Parker, M.W.
History
DepositionMay 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)48,10311
Polymers46,7562
Non-polymers1,3489
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-32 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.806, 89.994, 68.870
Angle α, β, γ (deg.)90.000, 98.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-321-

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: 23377.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAEES3, GST3, GSTP1 / Plasmid: PSE420 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P09211, glutathione transferase

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Non-polymers , 6 types, 386 molecules

#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-EAA / ETHACRYNIC ACID / Etacrynic acid


Mass: 303.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12Cl2O4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE DATA SUGGESTS THAT ETHACRAPLATIN BREAKS DOWN ON BINDING TO THE ENZYME SO THAT THE PLATINUM ...THE DATA SUGGESTS THAT ETHACRAPLATIN BREAKS DOWN ON BINDING TO THE ENZYME SO THAT THE PLATINUM MOIETY BINDS AT THE DIMER INTERFACE WITH TWO LIGANDS BEING CYS 101 FROM EACH MONOMER. THE ELECTRON DENSITY MAPS ARE CONSISTENT WITH CHLORINE BEING A THIRD LIGAND BUT THERE IS INSUFFICIENT DENSITY TO BUILD IN A FOURTH LIGAND. MODELING SUGGESTS THE FOURTH LIGAND COULD BE AN HYDROXYL OR WATER OR AMINE LIGAND

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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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM MES, pH 5.5, pH 6.0, 28% (w/v) PEG 8000, 20mM CaCl2 10mM DTT, 3mM EACPT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→20.28 Å / Num. all: 39483 / Num. obs: 39483 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.98 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16.9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.9 / Num. measured all: 20314 / Num. unique all: 5695 / Rsym value: 0.4 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: Difference Fourier
Starting model: 5GSS

5gss


Resolution: 1.85→20.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.868 / SU B: 2.848 / SU ML: 0.088 / SU R Cruickshank DPI: 0.137 / SU Rfree: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2026 5.1 %RANDOM
Rwork0.178 ---
obs0.18 39483 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.62 Å2 / Biso mean: 20.291 Å2 / Biso min: 7.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å2-0.68 Å2
2---0.79 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 67 377 3706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223431
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.0034661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29424.868152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70315573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8261516
X-RAY DIFFRACTIONr_chiral_restr0.1440.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022618
X-RAY DIFFRACTIONr_nbd_refined0.1980.21670
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2358
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.213
X-RAY DIFFRACTIONr_mcbond_it0.8731.52159
X-RAY DIFFRACTIONr_mcangle_it1.27623360
X-RAY DIFFRACTIONr_scbond_it2.10731479
X-RAY DIFFRACTIONr_scangle_it3.1354.51300
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 142 -
Rwork0.289 2720 -
all-2862 -
obs-20314 99.44 %

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