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- PDB-1grh: INHIBITION OF HUMAN GLUTATHIONE REDUCTASE BY THE NITROSOUREA DRUG... -

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Basic information

Entry
Database: PDB / ID: 1grh
TitleINHIBITION OF HUMAN GLUTATHIONE REDUCTASE BY THE NITROSOUREA DRUGS 1,3-BIS(2-CHLOROETHYL)-1-NITROSOUREA AND 1-(2-CHLOROETHYL)-3-(2-HYDROXYETHYL)-1-NITROSOUREA
ComponentsGLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME
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
ETHANOL / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsKarplus, P.A. / Schulz, G.E.
CitationJournal: 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.
History
DepositionDec 15, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Other
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5634
Polymers51,6361
Non-polymers9273
Water9,368520
1
A: GLUTATHIONE REDUCTASE
hetero molecules

A: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1268
Polymers103,2722
Non-polymers1,8536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area10570 Å2
ΔGint-73.4 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.800, 84.500, 63.200
Angle α, β, γ (deg.)90.00, 90.00, 58.70
Int Tables number5
Space group name H-MB112

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Components

#1: Protein GLUTATHIONE REDUCTASE


Mass: 51636.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / References: UniProt: P00390, EC: 1.6.4.2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 %satammonium sulfate1drop
330 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 3 Å
Details: IN AN ADDITIONAL EXPERIMENT THE REDUCED ENZYME WAS REACTED WITH HECNU IN SOLUTION AND THEN CRYSTALLIZED. DATA WERE COLLECTED TO ONLY 3.0 ANGSTROM RESOLUTION. THE MODIFIED ENZYME WAS ANALYZED ...Details: IN AN ADDITIONAL EXPERIMENT THE REDUCED ENZYME WAS REACTED WITH HECNU IN SOLUTION AND THEN CRYSTALLIZED. DATA WERE COLLECTED TO ONLY 3.0 ANGSTROM RESOLUTION. THE MODIFIED ENZYME WAS ANALYZED USING A DIFFERENCE FOURIER MAP WITHOUT REFINEMENT. THE COORDINATES OF THE RESULTING MODEL OF THE MODIFIED AMINO ACID RESIDUE CYS 58 (HECN-482) WERE INITIALLY GIVEN IN THIS ENTRY. IN ORDER TO BRING COMPLETENESS TO THE STRUCTURE, THE ENTRY HAS BEEN REMEDIATED BY MERGING THE COORDINATES OF THE ENTIRE MOLECULE FROM THE PDB ENTRY 1GRG, APART FROM THE COORDINATES OF RESIDUE 0A8 AND SUBSTITUTING IT BY THE COORDINATES OF CYS AND ETHANOL PRESENT IN THIS ENTRY.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 61 520 4080

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