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- PDB-1lb7: IGF-F1-1, A PEPTIDE ANTAGONIST OF IGF-1 -

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Basic information

Entry
Database: PDB / ID: 1lb7
TitleIGF-F1-1, A PEPTIDE ANTAGONIST OF IGF-1
ComponentsIGF-1 ANTAGONIST F1-1
KeywordsDE NOVO PROTEIN / loop-helix / disulfide
MethodSOLUTION NMR / distance geometry, molecular dynamics
AuthorsDeshayes, K. / Schaffer, M.L. / Skelton, N.J. / Nakamura, G.R. / Kadkhodayan, S. / Sidhu, S.S.
CitationJournal: Chem.Biol. / Year: 2002
Title: Rapid identification of small binding motifs with high-throughput phage display: discovery of peptidic antagonists of IGF-1 function.
Authors: Deshayes, K. / Schaffer, M.L. / Skelton, N.J. / Nakamura, G.R. / Kadkhodayan, S. / Sidhu, S.S.
History
DepositionApr 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGF-1 ANTAGONIST F1-1


Theoretical massNumber of molelcules
Total (without water)1,8791
Polymers1,8791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average,fewest violations,lowest energy,minimized average structure

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Components

#1: Protein/peptide IGF-1 ANTAGONIST F1-1


Mass: 1879.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: De novo sequence derived from phage display library
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D-ROESY
132COSY-35
1422D-ROESY
1521H-13C-HSQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques to generate distance (ROESY) and dihederal angle (DQF-COSY, COSY-35)restraints. Additional dihedral angle restraints were ...Text: This structure was determined using standard 2D homonuclear techniques to generate distance (ROESY) and dihederal angle (DQF-COSY, COSY-35)restraints. Additional dihedral angle restraints were derived from chemical shift information using the program TALOS

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Sample preparation

Details
Solution-IDContentsSolvent system
15.0 mM igf-f1-1 90%, H2O, 10% D2O, pH 5.1H2O
25.0 mM igf-f1-f, 100% D2O, pH* 5.1D2O
Sample conditionsIonic strength: 0 / pH: 5.1 / Pressure: atm / Temperature: 303 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
DGIIv98.0Havelrefinement
Discoverv98.0Accelrysrefinement
TALOSFeb 2000Delaglio & Baxrefinement
RefinementMethod: distance geometry, molecular dynamics / Software ordinal: 1
Details: The structures are based on 91 distance restraints and 26 dihedral angle restraints. None of the final structures have violations > 0.07A or 1.0 degrees. The mean rmsd to the mean ...Details: The structures are based on 91 distance restraints and 26 dihedral angle restraints. None of the final structures have violations > 0.07A or 1.0 degrees. The mean rmsd to the mean coordinates for heavy atoms of residues Cys3 to Tyr15 is 0.31+/-0.06 A.
NMR representativeSelection criteria: closest to the average,fewest violations,lowest energy,minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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