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- PDB-1d1f: SOLUTION STRUCTURE OF LACTAM-BRIDGED C-TERMINAL ANALOGUE-III OF N... -

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Basic information

Entry
Database: PDB / ID: 1d1f
TitleSOLUTION STRUCTURE OF LACTAM-BRIDGED C-TERMINAL ANALOGUE-III OF NEUROPEPTIDE Y
ComponentsC-TERMINAL ANALOGUE OF NEUROPEPTIDE Y, A POTENT Y2 RECEPTOR AGONIST
KeywordsNEUROPEPTIDE / LACTAM-BRIDGED / HELIX
MethodSOLUTION NMR / simulated annealing
AuthorsYao, S. / Norton, R.S.
Citation
Journal: J.Med.Chem. / Year: 2002
Title: Stabilization of the helical structure of Y2-selective analogues of neuropeptide Y by lactam bridges.
Authors: Yao, S. / Smith-White, M.A. / Potter, E.K. / Norton, R.S.
#1: Journal: To be Published
Title: Helical structure and self-association in a 13-residue neuropeptide Y Y2 receptor agonist: relationship to biological activity
Authors: Barnham, K.J. / Catalfamo, F. / Pallaghy, P.K. / Howlett, G.J. / Norton, R.S.
#2: Journal: J.Biomol.NMR / Year: 1996
Title: Solution structure of human neuropeptide Y
Authors: Monks, S.A. / Karagianis, G. / Howlett, G.J. / Norton, R.S.
History
DepositionSep 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations / Experimental preparation
Category: citation_author / pdbx_nmr_exptl_sample_conditions ...citation_author / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_nmr_exptl_sample_conditions.pressure_units

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-TERMINAL ANALOGUE OF NEUROPEPTIDE Y, A POTENT Y2 RECEPTOR AGONIST


Theoretical massNumber of molelcules
Total (without water)1,7761
Polymers1,7761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide C-TERMINAL ANALOGUE OF NEUROPEPTIDE Y, A POTENT Y2 RECEPTOR AGONIST


Mass: 1776.055 Da / Num. of mol.: 1 / Fragment: C-TERMINAL ANALOGUE / Mutation: L24A, I28K, T32E / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

DetailsContents: 4.0 MG IN 0.6ML H2O CONTAINING 30% TFE-D3 (BY VOLUME)
Sample conditionspH: 5.0 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR2.1BRUKERcollection
XEASY1.3BARTELSdata analysis
X-PLOR3.85BRUNGERstructure solution
X-PLOR3.85BRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURE WAS CALCULATED USING A TOTAL OF 114 UPPER BOUND DISTANCE RESTRAINTS AND 9 BACKBONE DIHEDRAL ANGLE CONSTRAINTS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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