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- PDB-1n6t: Solution Structure of the Tachykinin Peptide Neurokinin A -

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Basic information

Entry
Database: PDB / ID: 1n6t
TitleSolution Structure of the Tachykinin Peptide Neurokinin A
ComponentsNeurokinin A
KeywordsNEUROPEPTIDE / helix / 3 10 helix / lipid induced conformation / DPC micelles
Function / homologyTachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / neuropeptide signaling pathway / extracellular region / Neurokinin-A
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing(DYANA)
AuthorsChandrashekar, I.R. / Cowsik, S.M.
CitationJournal: Biophys.J. / Year: 2003
Title: Three-dimensional structure of the mammalian tachykinin peptide neurokinin A bound to lipid micelles.
Authors: Chandrashekar, I.R. / Cowsik, S.M.
History
DepositionNov 12, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_nmr_software ...citation / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_DOI / _pdbx_nmr_software.name
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurokinin A


Theoretical massNumber of molelcules
Total (without water)1,1361
Polymers1,1361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1280 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Neurokinin A


Mass: 1136.321 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in mammalian neuronal tissue.
References: UniProt: P19851

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 5mg of neurokinin A in 0.5ml of water (90% H2O, 10% D2O, pH 5.0)
Solvent system: 260mM perdeuterated DPC
Sample conditionsIonic strength: no salts used / pH: 5 / Pressure: ambient / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5P.Guntert, C.Mumenthaler, K.Wuthrichrefinement
XwinNMR3.1BRUKERprocessing
RefinementMethod: distance geometry, simulated annealing(DYANA) / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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