2IUH

Crystal structure of the PI3-kinase p85 N-terminal SH2 domain in complex with c-Kit phosphotyrosyl peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of the Pi 3-Kinase P85 Amino-Terminal Sh2 Domain and its Phosphopeptide Complexes

Nolte, R.T.Eck, M.J.Schlessinger, J.Shoelson, S.E.Harrison, S.C.

(1996) Nat Struct Biol 3: 364

  • DOI: 10.1038/nsb0496-364
  • Primary Citation of Related Structures:  
    2IUI, 2IUH, 2IUG

  • PubMed Abstract: 
  • Crystal structures of the amino-terminal SH2 domain of the p85alpha subunit of phosphatidylinositol (PI) 3-kinase, alone and in complex with phosphopeptides bearing pTyr-Met/Val-Xaa-Met motifs, show that phosphopeptides bind in the two-pronged manner ...

    Crystal structures of the amino-terminal SH2 domain of the p85alpha subunit of phosphatidylinositol (PI) 3-kinase, alone and in complex with phosphopeptides bearing pTyr-Met/Val-Xaa-Met motifs, show that phosphopeptides bind in the two-pronged manner seen in high-affinity Lck and Src SH2 complexes, with conserved interactions between the domain and the peptide segment from phosphotyrosine to Met+3. Peptide binding requires the rearrangement of a tyrosyl side chain in the BG loop to create the hydrophobic Met+3 binding pocket. The structures suggest a mechanism for the biological specificity exhibited by PI 3-kinase in its interactions with phosphoprotein partners.


    Organizational Affiliation

    Howard Hughes Medical Institute and Laboratory of Molecular Medicine, Children's Hospital, Boston, Massachusetts 02115, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNITA120Homo sapiensMutation(s): 0 
Gene Names: PIK3R1GRB1
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
NIH Common Fund Data Resources
PHAROS  P27986
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C-KIT PHOSPHOTYROSYL PEPTIDEB11Homo sapiensMutation(s): 0 
Gene Names: KITSCFR
EC: 2.7.10.1
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
NIH Common Fund Data Resources
PHAROS  P10721
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.95α = 90
b = 56.95β = 90
c = 68.17γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-06
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance