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- PDB-2k9e: NMR Solution Structure for ShK-192: A Potent KV1.3-Specific Immun... -

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Basic information

Entry
Database: PDB / ID: 2k9e
TitleNMR Solution Structure for ShK-192: A Potent KV1.3-Specific Immunosuppressive Polypeptide
ComponentsKappa-stichotoxin-She3a
KeywordsTOXIN / Protein / Ionic channel inhibitor / Nematocyst / Neurotoxin / Potassium channel inhibitor / Secreted
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 / simulated annealing, molecular dynamics
AuthorsGalea, C.A.
CitationJournal: Mol.Pharmacol. / Year: 2009
Title: Engineering a stable and selective peptide blocker of the Kv1.3 channel in T lymphocytes
Authors: Pennington, M.W. / Beeton, C. / Galea, C.A. / Smith, B.J. / Chi, V. / Monaghan, K.P. / Garcia, A. / Rangaraju, S. / Giuffrida, A. / Plank, D. / Crossley, G. / Nugent, D. / Khaytin, I. / ...Authors: Pennington, M.W. / Beeton, C. / Galea, C.A. / Smith, B.J. / Chi, V. / Monaghan, K.P. / Garcia, A. / Rangaraju, S. / Giuffrida, A. / Plank, D. / Crossley, G. / Nugent, D. / Khaytin, I. / Lefievre, Y. / Peshenko, I. / Dixon, C. / Chauhan, S. / Orzel, A. / Inoue, T. / Hu, X. / Moore, R.V. / Norton, R.S. / Chandy, K.G.
History
DepositionOct 9, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: 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 / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_src_syn / pdbx_nmr_sample_details / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_nmr_sample_details.contents / _pdbx_struct_mod_residue.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.db_code / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-stichotoxin-She3a


Theoretical massNumber of molelcules
Total (without water)4,4221
Polymers4,4221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area3320 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Kappa-stichotoxin-She3a / Kappa-SHTX-She3a / Potassium channel toxin ShK


Mass: 4422.172 Da / Num. of mol.: 1 / Mutation: M21(NLE) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in Stichodactyla helianthus
Source: (synth.) 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
2422D 1H-1H TOCSY
2522D 1H-13C HSQC
1612D 1H-1H COSY
1712D 1H-1H NOESY
2822D 1H-1H NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

Details
Solution-IDContentsSolvent system
13.0 mM ShK-192, 90% H2O/10% D2O90% H2O/10% D2O
23.0 mM ShK-192, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
3.0 mMShK-1921
3.0 mMShK-1922
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1104.79ambient 293 K
2104.1ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorechemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 639 / NOE intraresidue total count: 187 / NOE long range total count: 112 / NOE medium range total count: 157 / NOE sequential total count: 183
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 11

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