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- PDB-1mek: HUMAN PROTEIN DISULFIDE ISOMERASE, NMR, 40 STRUCTURES -

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Entry
Database: PDB / ID: 1mek
TitleHUMAN PROTEIN DISULFIDE ISOMERASE, NMR, 40 STRUCTURES
ComponentsPROTEIN DISULFIDE ISOMERASE
KeywordsELECTRON TRANSPORT / REDOX-ACTIVE CENTER / ISOMERASE / ENDOPLASMIC RETICULUM
Function / homology
Function and homology information


peptidyl-proline hydroxylation to 4-hydroxy-L-proline / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / insulin processing / VLDL assembly / thiol oxidase activity / procollagen-proline 4-dioxygenase activity / LDL remodeling / protein disulfide-isomerase / endoplasmic reticulum chaperone complex ...peptidyl-proline hydroxylation to 4-hydroxy-L-proline / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / insulin processing / VLDL assembly / thiol oxidase activity / procollagen-proline 4-dioxygenase activity / LDL remodeling / protein disulfide-isomerase / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Chylomicron assembly / interleukin-23-mediated signaling pathway / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / cellular response to interleukin-7 / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of T cell migration / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of cell adhesion / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / endoplasmic reticulum lumen / protein heterodimerization activity / external side of plasma membrane / focal adhesion / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / 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
Protein disulfide-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsKemmink, J. / Darby, N.J. / Dijkstra, K. / Nilges, M. / Creighton, T.E.
Citation
Journal: Biochemistry / Year: 1996
Title: Structure determination of the N-terminal thioredoxin-like domain of protein disulfide isomerase using multidimensional heteronuclear 13C/15N NMR spectroscopy.
Authors: Kemmink, J. / Darby, N.J. / Dijkstra, K. / Nilges, M. / Creighton, T.E.
#1: Journal: Protein Sci. / Year: 1995
Title: Nuclear Magnetic Resonance Characterization of the N-Terminal Thioredoxin-Like Domain of Protein Disulfide Isomerase
Authors: Kemmink, J. / Darby, N.J. / Dijkstra, K. / Scheek, R.M. / Creighton, T.E.
History
DepositionApr 16, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Assembly

Deposited unit
A: PROTEIN DISULFIDE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)13,2771
Polymers13,2771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / -
Representative

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Components

#1: Protein PROTEIN DISULFIDE ISOMERASE


Mass: 13276.909 Da / Num. of mol.: 1 / Fragment: PROLYL 4-HYDROXYLASE BETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-12 / Production host: Escherichia coli (E. coli) / References: UniProt: P07237, protein disulfide-isomerase
Has protein modificationY

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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

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: STRUCTURES WERE DETERMINED USING A HYBRID DISTANCE GEOMETRY/SIMULATED ANNEALING APPROACH (M. NILGES, G.M. CLORE, A.M. GRONENBORN, FEBS LETT. 229, 317, 1988). THE STRUCTURES ARE BASED ON 1270 ...Details: STRUCTURES WERE DETERMINED USING A HYBRID DISTANCE GEOMETRY/SIMULATED ANNEALING APPROACH (M. NILGES, G.M. CLORE, A.M. GRONENBORN, FEBS LETT. 229, 317, 1988). THE STRUCTURES ARE BASED ON 1270 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 34 HYDROGEN BOND DISTANCE RESTRAINTS DERIVED FROM 17 SLOWLY EXCHANGING AMIDE PROTONS AND OBSERVED NOE PATTERNS; AND 5 DISTANCE RESTRAINTS WHICH DEFINE THE DISULFIDE BOND BETWEEN CYS 36 AND CYS 39.
NMR ensembleConformers submitted total number: 40

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