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- PDB-2b19: Solution Structure of mammalian tachykinin peptide, Neuropeptide K -

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Basic information

Entry
Database: PDB / ID: 2b19
TitleSolution Structure of mammalian tachykinin peptide, Neuropeptide K
ComponentsNeuropeptide K
KeywordsNEUROPEPTIDE / helix / 3 10 helix / lipid induced conformation / DPC micelles
Function / homology
Function and homology information


neuromedin K receptor binding / substance K receptor binding / positive regulation of sensory perception of pain / positive regulation of corticosterone secretion / substance P receptor binding / insemination / : / : / positive regulation of flagellated sperm motility / positive regulation of saliva secretion ...neuromedin K receptor binding / substance K receptor binding / positive regulation of sensory perception of pain / positive regulation of corticosterone secretion / substance P receptor binding / insemination / : / : / positive regulation of flagellated sperm motility / positive regulation of saliva secretion / positive regulation of renal sodium excretion / Tachykinin receptors bind tachykinins / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / positive regulation of lymphocyte proliferation / tachykinin receptor signaling pathway / response to yeast / positive regulation of action potential / regulation of sensory perception of pain / positive regulation of acute inflammatory response / antifungal humoral response / response to morphine / positive regulation of ossification / negative regulation of systemic arterial blood pressure / negative regulation of heart rate / response to pain / positive regulation of epithelial cell migration / detection of temperature stimulus involved in sensory perception of pain / associative learning / neuropeptide signaling pathway / long-term memory / positive regulation of stress fiber assembly / sensory perception of pain / response to hormone / cellular response to nerve growth factor stimulus / positive regulation of synaptic transmission, GABAergic / regulation of blood pressure / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / antibacterial humoral response / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / G alpha (q) signalling events / killing of cells of another organism / defense response to Gram-negative bacterium / response to lipopolysaccharide / receptor ligand activity / defense response to Gram-positive bacterium / inflammatory response / G protein-coupled receptor signaling pathway / axon / innate immune response / neuronal cell body / synapse / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Tachykinin family / Tachykinin family / Tachykinin domain / Tachykinin family / Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature.
Similarity search - Domain/homology
Protachykinin-1 / Protachykinin-1
Similarity search - Component
MethodSOLUTION NMR / distance geometry, simulated annealing (DYANA)
AuthorsDike, A. / Cowsik, S.M.
CitationJournal: Biochemistry / Year: 2006
Title: Three-dimensional structure of neuropeptide k bound to dodecylphosphocholine micelles
Authors: Dike, A. / Cowsik, S.M.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuropeptide K


Theoretical massNumber of molelcules
Total (without water)3,9901
Polymers3,9901
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 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Neuropeptide K / NPK


Mass: 3989.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical Synthesis / References: UniProt: Q53GH4, UniProt: P20366*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 146mM perdeuterated DPC; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: No salts used / pH: 3.5 / Pressure: ambient / Temperature: 305 K

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NMR measurement

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.Wuthrichstructure solution
XwinNMR3.1BRUKERprocessing
DYANA1.5P.Guntert, C.Mumenthaler, K.Wuthrichrefinement
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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