4RTY

Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide APP12

• PDB DOI: https://doi.org/10.2210/pdb4RTY/pdb

• Classification: PROTEIN BINDING
• Organism(s): Gallus gallus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-16 Released: 2015-10-28 
• Deposition Author(s): Camara-Artigas, A., Bacarizo, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.137 
• R-Value Work: 0.116 
• R-Value Observed: 0.117 

Starting Model: experimental

Literature

Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide APP12

Camara-Artigas, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 8.41 kDa 
• Atom Count: 686 
• Modelled Residue Count: 71 
• Deposited Residue Count: 74 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	61	Gallus gallus	Mutation(s): 0  Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
APP12 peptide	B	13	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.137 
• R-Value Work: 0.116 
• R-Value Observed: 0.117 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.91	α = 90
b = 32.85	β = 104.45
c = 31.64	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Camara-Artigas, A., Bacarizo, J.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary