[English] 日本語
Yorodumi
- PDB-1gsy: GLUTATHIONE S-TRANSFERASE YFYF, CLASS PI, COMPLEXED WITH GLUTATHIONE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gsy
TitleGLUTATHIONE S-TRANSFERASE YFYF, CLASS PI, COMPLEXED WITH GLUTATHIONE
ComponentsGLUTATHIONE S-TRANSFERASE CLASS PI
KeywordsTRANSFERASE / MULTIGENE FAMILY
Function / homology
Function and homology information


cellular response to cell-matrix adhesion / negative regulation of neutrophil aggregation / negative regulation of peroxidase activity / Paracetamol ADME / Glutathione conjugation / negative regulation of smooth muscle cell chemotaxis / Detoxification of Reactive Oxygen Species / S-nitrosoglutathione binding / kinase regulator activity / response to L-ascorbic acid ...cellular response to cell-matrix adhesion / negative regulation of neutrophil aggregation / negative regulation of peroxidase activity / Paracetamol ADME / Glutathione conjugation / negative regulation of smooth muscle cell chemotaxis / Detoxification of Reactive Oxygen Species / S-nitrosoglutathione binding / kinase regulator activity / response to L-ascorbic acid / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / organic cyclic compound binding / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / oligodendrocyte development / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / linoleic acid metabolic process / negative regulation of leukocyte proliferation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / glutathione peroxidase activity / cellular response to glucocorticoid stimulus / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of vascular associated smooth muscle cell proliferation / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / toxic substance binding / response to amino acid / animal organ regeneration / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / cellular response to epidermal growth factor stimulus / Neutrophil degranulation / xenobiotic metabolic process / response to nutrient levels / regulation of ERK1 and ERK2 cascade / response to reactive oxygen species / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of ERK1 and ERK2 cascade / response to toxic substance / cellular response to insulin stimulus / response to estradiol / response to ethanol / cellular response to lipopolysaccharide / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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
GLUTATHIONE / Glutathione S-transferase P 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsParraga, A. / Garcia-Saez, I. / Coll, M.
CitationJournal: Biochem.J. / Year: 1998
Title: The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism.
Authors: Parraga, A. / Garcia-Saez, I. / Walsh, S.B. / Mantle, T.J. / Coll, M.
History
DepositionOct 25, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE CLASS PI
B: GLUTATHIONE S-TRANSFERASE CLASS PI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6234
Polymers47,0082
Non-polymers6152
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-15 kcal/mol
Surface area18160 Å2
MethodPISA
2
A: GLUTATHIONE S-TRANSFERASE CLASS PI
B: GLUTATHIONE S-TRANSFERASE CLASS PI
hetero molecules

A: GLUTATHIONE S-TRANSFERASE CLASS PI
B: GLUTATHIONE S-TRANSFERASE CLASS PI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2458
Polymers94,0164
Non-polymers1,2294
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area8690 Å2
ΔGint-43 kcal/mol
Surface area35090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.680, 162.570, 63.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein GLUTATHIONE S-TRANSFERASE CLASS PI / GST YFYF


Mass: 23503.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GLUTATHIONE COMMERCIALLY PROVIDED BY SIGMA / Source: (natural) Mus musculus (house mouse) / Organ: LIVER / References: UniProt: P19157, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.5 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.8 mMprotein1drop
250 mMMES1drop
38 %PEG60001drop
40.3 Msodium potassium phospahte1reservoir

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 20740
Reflection
*PLUS
% possible obs: 82.1 % / Num. measured all: 171889 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.44 Å / Lowest resolution: 2.5 Å / % possible obs: 50.3 % / Mean I/σ(I) obs: 3.3

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GLP

1glp


Resolution: 2.44→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.194 -
obs0.194 15756
Refinement stepCycle: LAST / Resolution: 2.44→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 40 131 3479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.594
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.208 / Rfactor Rfree: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.02

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more