Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.63 kDa 
• Atom Count: 725 
• Modelled Residue Count: 83 
• Deposited Residue Count: 85 
• Unique protein chains: 1

1PHT

PHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT SH3 DOMAIN, RESIDUES 1-85

• DOI: 10.2210/pdb1PHT/pdb

• Classification: PHOSPHOTRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1995-08-17 Released: 1995-12-07 
• Deposition Author(s): Liang, J., Chen, J.K., Schreiber, S.L., Clardy, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Crystal structure of P13K SH3 domain at 20 angstroms resolution.

Liang, J., Chen, J.K., Schreiber, S.T., Clardy, J.

(1996) J Mol Biol 257: 632-643

• PubMed: 8648629 
• DOI: 10.1006/jmbi.1996.0190
• Primary Citation of Related Structures:  
  1PHT


• PubMed Abstract: 
  

The P13K SH3 domain, residues 1 to 85 of the P1-3 kinase p85 subunit, has been characterized by X-ray diffraction. Crystals belonging to space group P4(3)2(1)2 diffract to 2.0 angstroms resolution and the structure was phased by single isomorphous replacement and anomalous scattering (SIRAS). As expected, the domain is a compact beta barrel with an over-all confirmation very similar to the independently determined NMR structures. The X-ray structure illuminates a discrepancy between the two NMR structures on the conformation of the loop region unique to P13K SH3. Furthermore, the ligand binding pockets of P13K SH3 domain are occupied by amino acid residues from symmetry-related P13K SH3 molecules: the C-terminal residues I(82) SPP of one and R18 of another. The interaction modes clearly resemble those observed for the P13K SH3 domain complexed with the synthetic peptide RLP1, a class 1 ligand, although there are significant differences. The solid-state interactions suggest a model of protein-protein aggregation that could be mediated by SH3 domains.

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Related Citations: 

• Structural Basis for the Binding of Proline-Rich Peptides to SH3 Domains
  Yu, H., Chen, J.K., Dalgarno, D.C., Brauer, A.W., Schreiber, S.L.
  (1994) Cell 76: 933

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Organizational Affiliation: 

Department of Chemistry, Baker Laboratory. Cornell University, Ithaca, NY 14853-1301, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT	A	85	Homo sapiens	Mutation(s): 0  Gene Names: PI3K SH3 FROM CDNA LIBRARY OF, PIK3R1, GRB1
Find proteins for P27986 (Homo sapiens) Explore P27986  Go to UniProtKB:  P27986
NIH Common Fund Data Resources
PHAROS:  P27986 GTEx:  ENSG00000145675

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47	α = 90
b = 47	β = 90
c = 92.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-08-17 
• Released Date: 1995-12-07 
Deposition Author(s): Liang, J., Chen, J.K., Schreiber, S.L., Clardy, J.

Revision History  

• Version 1.0: 1995-12-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance