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- PDB-1tru: THE HIGH-RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURES OF THE ... -

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Basic information

Entry
Database: PDB / ID: 1tru
TitleTHE HIGH-RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURES OF THE OXIDIZED AND REDUCED STATES OF HUMAN THIOREDOXIN
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 / cytosol / cytoplasm
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
AuthorsClore, G.M. / Qin, J. / Gronenborn, A.M.
CitationJournal: Structure / Year: 1994
Title: The high-resolution three-dimensional solution structures of the oxidized and reduced states of human thioredoxin.
Authors: Qin, J. / Clore, G.M. / Gronenborn, A.M.
History
DepositionMay 10, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

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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)11,6241
Polymers11,6241
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: CIS PROLINE - PRO 75 MODEL 1 / 2: CIS PROLINE - PRO 75 MODEL 2 / 3: CIS PROLINE - PRO 75 MODEL 3 / 4: CIS PROLINE - PRO 75 MODEL 4 / 5: CIS PROLINE - PRO 75 MODEL 5 / 6: CIS PROLINE - PRO 75 MODEL 6 / 7: CIS PROLINE - PRO 75 MODEL 7 / 8: CIS PROLINE - PRO 75 MODEL 8 / 9: CIS PROLINE - PRO 75 MODEL 9 / 10: CIS PROLINE - PRO 75 MODEL 10 / 11: CIS PROLINE - PRO 75 MODEL 11 / 12: CIS PROLINE - PRO 75 MODEL 12 / 13: CIS PROLINE - PRO 75 MODEL 13 / 14: CIS PROLINE - PRO 75 MODEL 14 / 15: CIS PROLINE - PRO 75 MODEL 15 / 16: CIS PROLINE - PRO 75 MODEL 16 / 17: CIS PROLINE - PRO 75 MODEL 17 / 18: CIS PROLINE - PRO 75 MODEL 18 / 19: CIS PROLINE - PRO 75 MODEL 19 / 20: CIS PROLINE - PRO 75 MODEL 20 / 21: CIS PROLINE - PRO 75 MODEL 21 / 22: CIS PROLINE - PRO 75 MODEL 22 / 23: CIS PROLINE - PRO 75 MODEL 23 / 24: CIS PROLINE - PRO 75 MODEL 24 / 25: CIS PROLINE - PRO 75 MODEL 25 / 26: CIS PROLINE - PRO 75 MODEL 26 / 27: CIS PROLINE - PRO 75 MODEL 27 / 28: CIS PROLINE - PRO 75 MODEL 28 / 29: CIS PROLINE - PRO 75 MODEL 29 / 30: CIS PROLINE - PRO 75 MODEL 30 / 31: CIS PROLINE - PRO 75 MODEL 31 / 32: CIS PROLINE - PRO 75 MODEL 32 / 33: CIS PROLINE - PRO 75 MODEL 33 / 34: CIS PROLINE - PRO 75 MODEL 34 / 35: CIS PROLINE - PRO 75 MODEL 35 / 36: CIS PROLINE - PRO 75 MODEL 36 / 37: CIS PROLINE - PRO 75 MODEL 37 / 38: CIS PROLINE - PRO 75 MODEL 38 / 39: CIS PROLINE - PRO 75 MODEL 39 / 40: CIS PROLINE - PRO 75 MODEL 40
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / -
Representative

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Components

#1: Protein THIOREDOXIN /


Mass: 11624.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P10599
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

RefinementSoftware ordinal: 1
Details: THE 3D STRUCTURE OF OXIDIZED HUMAN THIOREDOXIN IN SOLUTION BY NMR IS BASED ON 3018 EXPERIMENTAL RESTRAINTS COMPRISING: 2649 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS; 34 RESTRAINTS ...Details: THE 3D STRUCTURE OF OXIDIZED HUMAN THIOREDOXIN IN SOLUTION BY NMR IS BASED ON 3018 EXPERIMENTAL RESTRAINTS COMPRISING: 2649 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS; 34 RESTRAINTS FOR 17 H-BONDS INVOLVING 7 TIGHTLY BOUND WATER MOLECULES; 42 RESTRAINTS FOR 21 BACKBONE HYDROGEN BONDS INVOLVING SLOWLY EXCHANGING AMIDE PROTONS; 278 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1 AND 20 CHI2); AND 91 HN-HALPHA THREE-BOND COUPLING CONSTANTS. A COMPLETE LIST OF EXPERIMENTAL RESTRAINTS AND 1H, 13C AND 15N ASSIGNMENTS HAVE BEEN DEPOSITED WITH THE PROTEIN DATA BANK. THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT 229, 317 - 324. ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE. THE RESTRAINED MINIMIZED AVERAGE STRUCTURE (SA)R IS PRESENTED IN PROTEIN DATA BANK ENTRY 1TRS. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 40 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 1 - 105, AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. COLUMNS 61 - 65 OF THE COORDINATE RECORDS (THE B VALUE FIELD IN X-RAY STRUCTURES) IN THE MINIMIZED STRUCTURE (ENTRY 1TRS) GIVE THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE NUMBERS IN THIS FIELD OF THE INDIVIDUAL STRUCTURES (ENTRY 1TRU) HAVE NO MEANING.
NMR ensembleConformers submitted total number: 40

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