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Open data
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Basic information
Entry | Database: PDB / ID: 1pmx | ||||||
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Title | INSULIN-LIKE GROWTH FACTOR-I BOUND TO A PHAGE-DERIVED PEPTIDE | ||||||
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![]() | HORMONE/GROWTH FACTOR / ![]() ![]() | ||||||
Function / homology | ![]() glycolate metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Skelton, N.J. | ||||||
![]() | ![]() Title: Complex with a Phage Display-Derived Peptide Provides Insight into the Function of Insulin-like Growth Factor I Authors: Schaffer, M.L. / Deshayes, K. / Nakamura, G. / Sidhu, S. / Skelton, N.J. #1: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 544.1 KB | Display | ![]() |
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PDB format | ![]() | 472.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: Protein | Mass: 7663.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1879.216 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SEQUENCE DERIVED FROM PHAGE DISPLAY LIBRARY AND PREPARED BY CHEMICAL SYNTHESIS |
-Experimental details
-Experiment
Experiment | Method: ![]() | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE RESONANCE ASSIGNMENTS WERE DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 25 mM / pH: 5.1 / Pressure: 1 atm / Temperature: 313 K | ||||||||||||
Crystal grow![]() | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS, ![]() Details: THE COMPLEX WAS DETERMINED USING A TOTAL OF 905 NOE DISTANCE RESTRAINTS (146 INTRA RESIDUE, 203 SEQUENTIAL, 232 MEDIUM RANGE, 237 LONG-RANGE AND 87 INTERMOLECULAR), 24 HYDROGEN BOND ...Details: THE COMPLEX WAS DETERMINED USING A TOTAL OF 905 NOE DISTANCE RESTRAINTS (146 INTRA RESIDUE, 203 SEQUENTIAL, 232 MEDIUM RANGE, 237 LONG-RANGE AND 87 INTERMOLECULAR), 24 HYDROGEN BOND RESTRAINTS, 139 DIHEDRAL ANGLE RESTRAINTS (72 PHI, 44 PSI AND 23 CHI-1). THE BEST 20 CONFORMERS (OF 100) HAD NO DISTANCE VIOLATIONS GREATER THAN 0.11A AND NO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 1.5 DEGREES. RMSD FROM EXPERIMENTAL DISTANCE RESTRAINTS WAS 0.0049+/-0.0008. THE MEAN BACKBONE RMSD FROM THE MEAN STRUCTURE WAS 0.35 +/- 0.06 A FOR N, CA AND C ATOMS OF RESIDUES 3-26, 42-63 of IGF-I AND RESIDUES 3-15 OF THE PEPTIDE. 82% (17%) OF RESIDUES WERE IN THE MOST FAVOURED (ALLOWED) REGION OF PHI/PSI SPACE; NO RESIDUES WERE CONSISTENTLY IN THE DISALLOWED REGION. | ||||||||||||||||
NMR representative | Selection criteria: closest to the average, fewest violations | ||||||||||||||||
NMR ensemble | Conformer selection criteria: LEAST VIOLATION OF EXPERIMENTAL RESTRAINTS Conformers calculated total number: 100 / Conformers submitted total number: 20 |