Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.31 kDa 
• Atom Count: 1034 
• Residue Count: 114 
• Unique protein chains: 2

1H9O

PHOSPHATIDYLINOSITOL 3-KINASE, P85-ALPHA SUBUNIT: C-TERMINAL SH2 DOMAIN COMPLEXED WITH A TYR751 PHOSPHOPEPTIDE FROM THE PDGF RECEPTOR, CRYSTAL STRUCTURE AT 1.79 A

• DOI: 10.2210/pdb1H9O/pdb

• Classification: TRANSFERASE/RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-03-14 Released: 2001-03-19 
• Deposition Author(s): Pauptit, R.A., Rowsell, S., Breeze, A.L., Murshudov, G.N., Dennis, C.A., Derbyshire, D.J., Weston, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.219 
• R-Value Work: 0.163 
• R-Value Observed: 0.168 

Literature

NMR Trial Models: Experiences with the Colicin Immunity Protein Im7 and the P85Alpha C-Terminal Sh2-Peptide Complex

Pauptit, R.A., Dennis, C.A., Derbyshire, D.J., Breeze, A.L., Weston, S.A., Rowsell, S., Murshudov, G.N.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1397

• PubMed: 11567151 
• DOI: 10.1107/s0907444901012434
• Primary Citation of Related Structures:  
  1H9O


• PubMed Abstract: 
  

Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85alpha subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excised. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. The challenges typical of the use of NMR trial models in molecular replacement are discussed.

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Organizational Affiliation: 

AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, England. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATIDYLINOSITOL 3-KINASE	A	112	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R1, GRB1
Find proteins for P27986 (Homo sapiens) Explore P27986  Go to UniProtKB:  P27986
NIH Common Fund Data Resources
PHAROS:  P27986 GTEx:  ENSG00000145675

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-PLATELET-DERIVED GROWTH FACTOR RECEPTOR	B	5	Homo sapiens	Mutation(s): 0  Gene Names: PDGFRB, PDGFR, PDGFR1 EC: 2.7.10.1
Find proteins for P09619 (Homo sapiens) Explore P09619  Go to UniProtKB:  P09619
NIH Common Fund Data Resources
PHAROS:  P09619 GTEx:  ENSG00000113721

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.219 
• R-Value Work: 0.163 
• R-Value Observed: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59	α = 90
b = 32.8	β = 96.2
c = 54.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-03-14 
• Released Date: 2001-03-19 
Deposition Author(s): Pauptit, R.A., Rowsell, S., Breeze, A.L., Murshudov, G.N., Dennis, C.A., Derbyshire, D.J., Weston, S.A.

Revision History 

• Version 1.0: 2001-03-19
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection