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- PDB-4trx: HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF REDUCED RECOMBINAN... -

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Basic information

Entry
Database: PDB / ID: 4trx
TitleHIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF REDUCED RECOMBINANT HUMAN THIOREDOXIN IN SOLUTION
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide ...Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / positive regulation of DNA binding / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsForman-Kay, J.D. / Clore, G.M. / Gronenborn, A.M.
Citation
Journal: Biochemistry / Year: 1991
Title: High-resolution three-dimensional structure of reduced recombinant human thioredoxin in solution.
Authors: Forman-Kay, J.D. / Clore, G.M. / Wingfield, P.T. / Gronenborn, A.M.
#1: Journal: Biochemistry / Year: 1990
Title: Studies on the Solution Conformation of Human Thioredoxin Using Heteronuclear 15N-1H Nuclear Magnetic Resonance Spectroscopy
Authors: Forman-Kay, J.D. / Gronenborn, A.M. / Kay, L.E. / Wingfield, P.T. / Clore, G.M.
#2: Journal: Biochemistry / Year: 1989
Title: A Proton Nuclear Magnetic Resonance Assignment and Secondary Structure Determination of Recombinant Human Thioredoxin
Authors: Forman-Kay, J.D. / Clore, G.M. / Driscoll, P.C. / Wingfield, P. / Richards, F.M. / Gronenborn, A.M.
History
DepositionDec 17, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)11,7201
Polymers11,7201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: RESIDUE PRO 75 IS A CIS PROLINE.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)33 / -
Representative

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Components

#1: Protein THIOREDOXIN


Mass: 11720.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P10599

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

RefinementSoftware ordinal: 1
Details: STRUCTURES DETERMINED BY THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD OF M. NILGES, G. M. CLORE, AND A. M. GRONENBORN (FEBS LETT. 229, 317 (1988)). THE ...Details: STRUCTURES DETERMINED BY THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD OF M. NILGES, G. M. CLORE, AND A. M. GRONENBORN (FEBS LETT. 229, 317 (1988)). THE STRUCTURES ARE BASED ON 1983 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 52 HYDROGEN-BONDING DISTANCE RESTRAINTS FOR 26 HYDROGEN-BONDS IDENTIFIED ON THE BASIS OF THE NOE AND AMIDE PROTON EXCHANGE DATA, AS WELL AS THE INITIAL STRUCTURE CALCULATIONS; AND 98 PHI AND 71 PSI BACKBONE TORSION ANGLE RESTRAINTS AND 72 CHI1 SIDE-CHAIN TORSION ANGLE RESTRAINTS DERIVED FROM COUPLING CONSTANTS AND NOE DATA. A TOTAL OF 33 STRUCTURES WERE CALCULATED. THIS ENTRY REPRESENTS THE ENTIRE SET OF 33 STRUCTURES. THE MINIMIZED AVERAGE STRUCTURE CAN BE FOUND IN PDB ENTRY 3TRX. THIS AVERAGED STRUCTURE IS OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE NUMBERS IN THE LAST COLUMN OF THIS COORDINATE FILE ARE MEANINGLESS.
NMR ensembleConformers submitted total number: 33

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