[English] 日本語
Yorodumi
- PDB-9vfa: GSTM1 in complex with GSH and bithionol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vfa
TitleGSTM1 in complex with GSH and bithionol
ComponentsGlutathione S-transferase Mu 1
KeywordsTRANSFERASE / GST / inhibitor
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / glutathione transferase ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / glutathione metabolic process / enzyme binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione transferase family / 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, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione transferase family / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
2,2'-sulfanediylbis(4,6-dichlorophenol) / GLUTATHIONE / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSun, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81502629 China
CitationJournal: To Be Published
Title: Bithionol Targets GSTs to Increase Oxidative Stress and Enhance Doxorubicin Efficacy
Authors: Sun, Q.
History
DepositionJun 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione S-transferase Mu 1
B: Glutathione S-transferase Mu 1
C: Glutathione S-transferase Mu 1
D: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,66510
Polymers102,9874
Non-polymers1,6776
Water7,494416
1
A: Glutathione S-transferase Mu 1
B: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4645
Polymers51,4942
Non-polymers9713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-23 kcal/mol
Surface area19340 Å2
MethodPISA
2
C: Glutathione S-transferase Mu 1
D: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2005
Polymers51,4942
Non-polymers7073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-23 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.129, 83.799, 213.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Glutathione S-transferase Mu 1 / GST HB subunit 4 / GST class-mu 1 / GSTM1-1 / GSTM1a-1a / GSTM1b-1b / GTH4


Mass: 25746.842 Da / Num. of mol.: 4 / Fragment: Ran Binding Domain
Mutation: D537G, T539C, V540E, K541Q, Y1022C, 377-413 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM1, GST1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09488, glutathione transferase
#2: Chemical
ChemComp-GSH / Glutathione


Type: peptide-like / Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-B1T / 2,2'-sulfanediylbis(4,6-dichlorophenol)


Mass: 356.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H6Cl4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Amino acids, 0.1 M MES pH 6.0 - 7.0, 40%-50% Mix1(Mix1: 40% v/v PEG550*MME, 20% w/v PEG20000)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→50.01 Å / Num. obs: 55890 / % possible obs: 98.7 % / Redundancy: 8.6 % / CC1/2: 0.337 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.039 / Net I/σ(I): 13
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.9 % / Num. unique obs: 2642 / CC1/2: 0.337 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6a38

6a38


Resolution: 2.15→41.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 18.173 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 2827 5.1 %RANDOM
Rwork0.22818 ---
obs0.2295 53015 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.164 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0 Å2
2---0.4 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.15→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7248 0 105 416 7769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0127545
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167130
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.8610170
X-RAY DIFFRACTIONr_angle_other_deg0.3681.77616510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.452548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.482101376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021724
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.152.6633484
X-RAY DIFFRACTIONr_mcbond_other1.152.6633484
X-RAY DIFFRACTIONr_mcangle_it2.034.784348
X-RAY DIFFRACTIONr_mcangle_other2.034.7824349
X-RAY DIFFRACTIONr_scbond_it1.2812.8434061
X-RAY DIFFRACTIONr_scbond_other1.2812.8434060
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.185.175823
X-RAY DIFFRACTIONr_long_range_B_refined6.31327.248702
X-RAY DIFFRACTIONr_long_range_B_other6.27726.398639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 196 -
Rwork0.451 3665 -
obs--93.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.46450.60210.09090.93780.66042.82860.144-0.22430.03990.1138-0.1320.03160.20460.0647-0.0120.3737-0.0466-0.02390.3759-0.06040.0129-3.634-11.62691.908
21.03440.63510.24590.7670.27731.83670.00380.0212-0.0422-0.27730.10640.0245-0.00820.1729-0.11020.4538-0.0119-0.01030.2061-0.03160.0313-0.156-11.10767.321
31.3492-1.06630.79181.749-0.67081.20530.16040.2408-0.1904-0.0631-0.17570.2762-0.02460.24420.01530.34070.0078-0.01550.2259-0.01450.0962-26.464-13.73714.561
40.9282-0.89040.49360.9715-0.42421.8669-0.1586-0.0949-0.16260.31950.16880.1094-0.327-0.0974-0.01020.53180.044-0.02830.20140.02310.0678-26.756-9.4138.994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B1 - 218
4X-RAY DIFFRACTION2B301 - 302
5X-RAY DIFFRACTION3C1 - 218
6X-RAY DIFFRACTION3C301 - 302
7X-RAY DIFFRACTION4D1 - 218
8X-RAY DIFFRACTION4D301

+
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