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- PDB-1p9f: NMR Structure of Neurokinin B from DYANA -

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Basic information

Entry
Database: PDB / ID: 1p9f
TitleNMR Structure of Neurokinin B from DYANA
ComponentsNEUROKININ B
KeywordsNEUROPEPTIDE / protein / Structures from DYANA
Function / homology
Function and homology information


Tachykinin receptors bind tachykinins / tachykinin receptor signaling pathway / positive regulation of blood pressure / neuropeptide signaling pathway / female pregnancy / G alpha (q) signalling events / signaling receptor binding / extracellular space / extracellular region
Similarity search - Function
Neurokinin-B/Tachykinin-3 / Neurokinin B / Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature.
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry, molecular dynamics
AuthorsMantha, A.K. / Chandrashekar, I.R. / Baquer, N.Z. / Cowsik, S.M.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2004
Title: Three dimensional structure of Mammalian tachykinin Peptide neurokinin B bound to lipid micelles.
Authors: Mantha, A.K. / Chandrashekar, I.R. / Baquer, N.Z. / Cowsik, S.M.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 22, 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: NEUROKININ B


Theoretical massNumber of molelcules
Total (without water)1,2121
Polymers1,2121
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 / -structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide NEUROKININ B / NKB / Neuromedin K / ZNEUROK1


Mass: 1212.417 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (humans).
References: UniProt: Q9UHF0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 2.5mg in 500ul of 90% water and 10%D20 and 47mg of DPC
Solvent system: aueous phase
Sample conditionspH: 2.5 / Temperature: 305 K

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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
XwinNMR2.6Brukerdata analysis
DYANA1.5Peter Guntertstructure solution
DYANA1.5Peter Guntertrefinement
RefinementMethod: distance geometry, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers submitted total number: 20

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