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- PDB-1in2: Peptide Antagonist of IGFBP1, (i,i+7) Covalently Restrained Analog -

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Basic information

Entry
Database: PDB / ID: 1in2
TitlePeptide Antagonist of IGFBP1, (i,i+7) Covalently Restrained Analog
ComponentsIGFBP-1 antagonist
KeywordsANTAGONIST / covalently constrained helix
Function / homologyPENTANE
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsSkelton, N.J. / Chen, Y.M. / Dubree, N. / Quan, C. / Jackson, D.Y. / Cochran, A.G. / Zobel, K. / Deshayes, K. / Baca, M. / Pisabarro, M.T. / Lowman, H.B.
Citation
Journal: Biochemistry / Year: 2001
Title: Structure-function analysis of a phage display-derived peptide that binds to insulin-like growth factor binding protein 1.
Authors: Skelton, N.J. / Chen, Y.M. / Dubree, N. / Quan, C. / Jackson, D.Y. / Cochran, A. / Zobel, K. / Deshayes, K. / Baca, M. / Pisabarro, M.T. / Lowman, H.B.
#1: Journal: Biochemistry / Year: 1998
Title: Molecular Mimics of Insulin-like Growth Factor 1 (IGF-1) for Inhibiting IGF-1: IGF-Binding Protein Interactions
Authors: Lowman, H.B. / Chen, Y.M. / Skelton, N.J. / Mortensen, D.L. / Tomlinson, E.E. / Sadick, M.D. / Robinson, I.C. / Clark, R.G.
History
DepositionMay 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGFBP-1 antagonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7152
Polymers1,6431
Non-polymers721
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 #1fewest violations

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Components

#1: Protein/peptide IGFBP-1 antagonist


Mass: 1642.879 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. It was designed from sequence selected from a phage display library.
#2: Chemical ChemComp-LNK / PENTANE


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-ROESY
121DQF-COSY
2322D-ROESY
242COSY-35
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM peptide90% H2O/10% D2O
25 mM peptide100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1051 atm303 K
2051 atm303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix970msidata analysis
DGII970havelrefinement
Discover970msirefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
Details: The structure was detemined on the basis of 138 NOE distance restraints and 11 dihedral angle restraints. The resulting ensemble had no restraint violations greater than 0.07 Angstroms or 1. ...Details: The structure was detemined on the basis of 138 NOE distance restraints and 11 dihedral angle restraints. The resulting ensemble had no restraint violations greater than 0.07 Angstroms or 1.4 deg. The mean restraint violation energy was 0.04 +/- 0.03 kcal/mol.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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