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- PDB-5djl: Structure of WT Human Glutathione Transferase in complex with cis... -

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Basic information

Entry
Database: PDB / ID: 5djl
TitleStructure of WT Human Glutathione Transferase in complex with cisplatin in the presence of glutathione.
ComponentsGlutathione S-transferase P
Keywordstransferase/transferase inhibitor / Anticancer Cisplatin Glutathione / transferase-transferase inhibitor complex
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / kinase regulator activity / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of JUN kinase activity ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / kinase regulator activity / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of JUN kinase activity / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / nitric oxide binding / JUN kinase binding / glutathione peroxidase activity / Paracetamol ADME / 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 MAP kinase activity / negative regulation of MAPK cascade / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / positive regulation of superoxide anion generation / central nervous system development / fatty acid binding / negative regulation of protein kinase activity / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
CARBONATE ION / GLUTATHIONE / : / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsParker, L.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A structure-based mechanism of cisplatin resistance mediated by Glutathione Transferase P1-1
Authors: Parker, L.J. / Italiano, L.C. / Hancock, N.C. / Aitken, J. / Harris, H.H. / Hansen, G. / Ascher, D.B. / Morton, C.J. / Parker, M.W. / Lo Bello, M.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.3Sep 27, 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
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_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.ptnr2_symmetry / _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_conn.ptnr2_symmetry

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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)48,58213
Polymers46,7562
Non-polymers1,82711
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-107 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.450, 89.940, 68.780
Angle α, β, γ (deg.)90.000, 98.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-574-

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: GSTP1, FAEES3, GST3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase

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Non-polymers , 7 types, 539 molecules

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


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100MM MES, PH 5.5, PH 6.0, 28% (W/V) PEG 8000, 20MM CACL2 10MM DTT, 10MM GSH. Soaked in 0.1MM Cisplatin for 24hrs.

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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: Nov 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→31.58 Å / Num. obs: 43040 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 17.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.041 / Net I/σ(I): 9.6 / Num. measured all: 175670 / Scaling rejects: 149
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.8-1.8440.5062.9989924770.8370.28898.4
9-31.583.50.03417.612723620.9890.02497.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.4data scaling
MOSFLMdata reduction
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GSS

5gss


Resolution: 1.8→29.178 Å / FOM work R set: 0.9053 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 2077 4.83 %Random Selection
Rwork0.1494 40917 --
obs0.1507 42994 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.07 Å2 / Biso mean: 20.66 Å2 / Biso min: 7.72 Å2
Refinement stepCycle: final / Resolution: 1.8→29.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 134 528 3946
Biso mean--28.6 29.05 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043435
X-RAY DIFFRACTIONf_angle_d0.9554663
X-RAY DIFFRACTIONf_chiral_restr0.048514
X-RAY DIFFRACTIONf_plane_restr0.003602
X-RAY DIFFRACTIONf_dihedral_angle_d12.5521283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84190.24671410.222647278899
1.8419-1.88790.27091300.21022729285999
1.8879-1.9390.23381270.19922684281199
1.939-1.9960.18991520.17672689284199
1.996-2.06040.2291440.18062757290199
2.0604-2.1340.22341430.166126982841100
2.134-2.21950.18151310.145827362867100
2.2195-2.32040.17311340.138827112845100
2.3204-2.44270.16521390.135127522891100
2.4427-2.59570.15611210.131327612882100
2.5957-2.79590.16761470.144127442891100
2.7959-3.0770.19021490.152627302879100
3.077-3.52160.17091400.1427642904100
3.5216-4.43440.13951320.124127482880100
4.4344-29.18190.15091470.14832767291498

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