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- PDB-1alg: SOLUTION STRUCTURE OF AN HGR INHIBITOR, NMR, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1alg
TitleSOLUTION STRUCTURE OF AN HGR INHIBITOR, NMR, 10 STRUCTURES
ComponentsP11
KeywordsOXIDOREDUCTASE / HUMAN GLUTATHIONE REDUCTASE / PROTEIN-DIMERIZATION INHIBITOR
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 / cellular response to oxidative stress / NADP binding / 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, class I / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsSchott, M.K. / Nordhoff, A. / Becker, K. / Kalbitzer, H.R. / Schirmer, R.H.
CitationJournal: Eur.J.Biochem. / Year: 1997
Title: Denaturation and reactivation of dimeric human glutathione reductase--an assay for folding inhibitors.
Authors: Nordhoff, A. / Tziatzios, C. / van den Broek, J.A. / Schott, M.K. / Kalbitzer, H.R. / Becker, K. / Schubert, D. / Schirmer, R.H.
History
DepositionJun 3, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P11


Theoretical massNumber of molelcules
Total (without water)2,4431
Polymers2,4431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50NO VIOLATION, SMALL ENERGY
Representative

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Components

#1: Protein/peptide P11


Mass: 2442.829 Da / Num. of mol.: 1 / Fragment: INTERSUBUNIT-CONTACT HELIX
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / References: UniProt: P00390, EC: 1.6.4.2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131COSY

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Sample preparation

Sample conditionspH: 3.1 / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
XwinNMRstructure solution
AURELIAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: SIMULATED-ANNEALING PROTOCOL STARTING WITH 50 RANDOM STRUCTURES. 236 DISTANCE CONSTRAINTS. ENERGY MINIMIZED (2000 CYCLES), SUBJECTED TO ROOM-TEMPERATURE-RESTRAINED MOLECULAR DYNAMICS (20PS) ...Details: SIMULATED-ANNEALING PROTOCOL STARTING WITH 50 RANDOM STRUCTURES. 236 DISTANCE CONSTRAINTS. ENERGY MINIMIZED (2000 CYCLES), SUBJECTED TO ROOM-TEMPERATURE-RESTRAINED MOLECULAR DYNAMICS (20PS) AND ENERGY MINIMIZED AGAIN (2000 CYCLES). AFTER THIS, NO DISTANCE OR DIHEDRAL-ANGLE CONSTRAINTS WERE VIOLATED. FINAL REFINEMENT: ENERGY MINIMIZATION ON THE BASIS OF THE COMPLETE EMPIRICAL-ENERGY FUNCTION (DEFAULT PARAMETERS BUT DIELECTRIC CONSTANT E OF 3) INCLUDING THE ELECTROSTATIC INTERACTIONS.
NMR ensembleConformer selection criteria: NO VIOLATION, SMALL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 10

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