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- PDB-1bwc: STRUCTURE OF HUMAN GLUTATHIONE REDUCTASE COMPLEXED with AJOENE IN... -

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Basic information

Entry
Database: PDB / ID: 1bwc
TitleSTRUCTURE OF HUMAN GLUTATHIONE REDUCTASE COMPLEXED with AJOENE INHIBITOR AND SUBVERSIVE SUBSTRATE
ComponentsPROTEIN (GLUTATHIONE REDUCTASE)
KeywordsOXIDOREDUCTASE / FLAVOENZYME / REDOX-ACTIVE CENTER
Function / homology
Function and homology information


glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / flavin adenine dinucleotide binding ...glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / flavin adenine dinucleotide binding / NADP binding / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / external side of plasma membrane / mitochondrion / extracellular exosome / cytosol
Similarity search - Function
Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily ...Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(PROP-2-ENE-1-SULFINYL)-PROPENE-1-THIOL / FLAVIN-ADENINE DINUCLEOTIDE / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGallwitz, H. / Bonse, S. / Martinez-Cruz, A. / Schlichting, I. / Schumacher, K. / Krauth-Siegel, R.L.
Citation
Journal: J.Med.Chem. / Year: 1999
Title: Ajoene is an inhibitor and subversive substrate of human glutathione reductase and Trypanosoma cruzi trypanothione reductase: crystallographic, kinetic, and spectroscopic studies.
Authors: Gallwitz, H. / Bonse, S. / Martinez-Cruz, A. / Schlichting, I. / Schumacher, K. / Krauth-Siegel, R.L.
#1: Journal: Eur.J.Biochem. / Year: 1988
Title: Inhibition of Human Glutathione Reductase by the Nitrosourea Drugs 1,3-Bis(2- Chloroethyl)-1-Nitrosourea and 1-(2-Chloroethyl)-3-(2-Hydroxyethyl)-1- Nitrosourea. A Crystallographic Analysis
Authors: Karplus, P.A. / Krauth-Siegel, R.L. / Schirmer, R.H. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Refined Structure of Glutathione Reductase at 1.54 A Resolution
Authors: Karplus, P.A. / Schulz, G.E.
History
DepositionSep 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GLUTATHIONE REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6204
Polymers51,6361
Non-polymers9833
Water2,558142
1
A: PROTEIN (GLUTATHIONE REDUCTASE)
hetero molecules

A: PROTEIN (GLUTATHIONE REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2398
Polymers103,2722
Non-polymers1,9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10890 Å2
ΔGint-106 kcal/mol
Surface area36350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.300, 146.900, 128.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (GLUTATHIONE REDUCTASE) / GR


Mass: 51636.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: ERYTHROCYTES / Gene: GOR / Gene (production host): GOR / Production host: Escherichia coli (E. coli) / Strain (production host): SG5 / References: UniProt: P00390, EC: 1.6.4.2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-AJ3 / 3-(PROP-2-ENE-1-SULFINYL)-PROPENE-1-THIOL


Mass: 162.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10OS2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGLUTATHIONE REDUCTASE IS ACTIVE AS A DIMER OF TWO IDENTICAL SUBUNITS, WHICH ARE COVALENTLY ...GLUTATHIONE REDUCTASE IS ACTIVE AS A DIMER OF TWO IDENTICAL SUBUNITS, WHICH ARE COVALENTLY CONNECTED BY AN INTERMOLECULAR CYS 90 - CYS 90' DISULFIDE BOND.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growpH: 6.9 / Details: pH 6.9
Crystal grow
*PLUS
Temperature: 4-25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5-10 mg/mlprotein1drop
270-90 %(E)-ajoene1drop
35 %ammonium sulfate1drop
417 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Jun 1, 1997 / Details: MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 34707 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.117
Reflection shellResolution: 2.1→2.2 Å / % possible all: 74.6
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 147210

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Processing

Software
NameVersionClassification
XDSdata scaling
AMoREphasing
X-PLOR3.851refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GRE

1gre


Resolution: 2.1→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2372 7.1 %RANDOM
Rwork0.18 ---
obs0.18 33205 92.3 %-
Displacement parametersBiso mean: 22.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 63 142 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg0.925
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.083
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.171.5
X-RAY DIFFRACTIONx_mcangle_it1.912
X-RAY DIFFRACTIONx_scbond_it2.22
X-RAY DIFFRACTIONx_scangle_it3.342.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.338 220 6.7 %
Rwork0.285 3082 -
obs--74.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3FAD.PARFAD.TOP
X-RAY DIFFRACTION4AJO3.PARMAJO3.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.1 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.083
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.338 / % reflection Rfree: 6.7 % / Rfactor Rwork: 0.285

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