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- PDB-1bei: Shk-dnp22: A Potent Kv1.3-specific immunosuppressive polypeptide,... -

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Basic information

Entry
Database: PDB / ID: 1bei
TitleShk-dnp22: A Potent Kv1.3-specific immunosuppressive polypeptide, NMR, 20 structures
ComponentsPOTASSIUM CHANNEL TOXIN SHK
KeywordsPOTASSIUM CHANNEL INHIBITOR / SEA ANEMONE / IMMUNOSUPPRESSANT NEUROTOXIN
Function / homologyShKT domain / ShKT domain profile. / nematocyst / potassium channel regulator activity / toxin activity / defense response to bacterium / extracellular region / Kappa-stichotoxin-She3a
Function and homology information
Biological speciesStichodactyla helianthus (sea anemone)
MethodSOLUTION NMR / distance geometry
AuthorsKalman, K. / Pennington, M.W. / Lanigan, M.D. / Nguyen, A. / Rauer, H. / Mahnir, V. / Gutman, G.A. / Paschetto, K. / Kem, W.R. / Grissmer, S. ...Kalman, K. / Pennington, M.W. / Lanigan, M.D. / Nguyen, A. / Rauer, H. / Mahnir, V. / Gutman, G.A. / Paschetto, K. / Kem, W.R. / Grissmer, S. / Christian, E.P. / Cahalan, M.D. / Norton, R.S. / Chandy, K.G.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: ShK-Dap22, a potent Kv1.3-specific immunosuppressive polypeptide.
Authors: Kalman, K. / Pennington, M.W. / Lanigan, M.D. / Nguyen, A. / Rauer, H. / Mahnir, V. / Paschetto, K. / Kem, W.R. / Grissmer, S. / Gutman, G.A. / Christian, E.P. / Cahalan, M.D. / Norton, R.S. / Chandy, K.G.
History
DepositionMay 14, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_conn
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
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POTASSIUM CHANNEL TOXIN SHK


Theoretical massNumber of molelcules
Total (without water)4,0281
Polymers4,0281
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)20 / 50LOWEST STEREOCHEMICAL ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide POTASSIUM CHANNEL TOXIN SHK / SHK-DNP22


Mass: 4027.813 Da / Num. of mol.: 1
Mutation: K22DNP, DIAMINOPROPANOATE (DNP) SUBSTITUTION AT POSITION 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stichodactyla helianthus (sea anemone) / References: UniProt: P29187

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
141E-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 2D NMR SPECTROSCOPY ON SYNTHETIC SHK-DNP22

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Sample preparation

DetailsContents: 10% D2O OR 100% D2O
Sample conditionspH: 4.9 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
DYANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: STRUCTURES REFINED USING SIMULATED ANNEALING FOLLOWED BY CHARMM MINIMISATION
NMR ensembleConformer selection criteria: LOWEST STEREOCHEMICAL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 20

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