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- PDB-4hj2: Crystal Structure Analysis of GSTA1-1 in complex with chlorambucil -

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Basic information

Entry
Database: PDB / ID: 4hj2
TitleCrystal Structure Analysis of GSTA1-1 in complex with chlorambucil
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / alpha-beta
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / linoleic acid metabolic process / steroid delta-isomerase activity / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / linoleic acid metabolic process / steroid delta-isomerase activity / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / epithelial cell differentiation / glutathione metabolic process / xenobiotic metabolic process / fatty acid binding / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha 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, alpha 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-LZ6 / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKarpusas, M. / Chiniadis, L. / Labrou, N.E.
CitationJournal: Plos One / Year: 2013
Title: The interaction of the chemotherapeutic drug chlorambucil with human glutathione transferase A1-1: kinetic and structural analysis.
Authors: Karpusas, M. / Axarli, I. / Chiniadis, L. / Papakyriakou, A. / Bethanis, K. / Scopelitou, K. / Clonis, Y.D. / Labrou, N.E.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 A1
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2194
Polymers50,0692
Non-polymers1,1502
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-21 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.000, 93.530, 51.180
Angle α, β, γ (deg.)90.000, 93.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21A-544-

HOH

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Components

#1: Protein Glutathione S-transferase A1 / GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1


Mass: 25034.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08263, glutathione transferase
#2: Chemical ChemComp-LZ6 / L-gamma-glutamyl-S-(2-{[4-(3-carboxypropyl)phenyl](2-chloroethyl)amino}ethyl)-L-cysteinylglycine / Chlorambucil-Glutathione Conjugate


Mass: 575.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H35ClN4O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.36 Å3/Da / Density % sol: 47.9 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23814 / % possible obs: 87.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.05 / Χ2: 0.651 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1820.22923340.588184.9
2.18-2.261.80.18517670.646165
2.26-2.372.10.16221790.588180.5
2.37-2.492.20.12924180.649189.6
2.49-2.652.30.10124970.654191.6
2.65-2.852.30.08125300.667192.1
2.85-3.142.30.06125510.715194.1
3.14-3.592.30.04325680.677193.6
3.59-4.522.30.03323780.676187.2
4.52-502.40.02525920.617192.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.49 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.258 1838 6.8 %
Rwork0.2147 --
obs-23318 85.6 %
Solvent computationBsol: 28.1301 Å2
Displacement parametersBiso max: 74.58 Å2 / Biso mean: 29.39 Å2 / Biso min: 8.06 Å2
Baniso -1Baniso -2Baniso -3
1--2.502 Å20 Å24.722 Å2
2--4.629 Å20 Å2
3----2.127 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 76 298 3864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.346
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION23CSH_on_r1_aduct1_prodrg.parm
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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