4RTW | pdb_00004rtw

Crystal structure of the c-Src-SH3 domain E93V/Q128R mutant in complex with the high affinity peptide APP12

• PDB DOI: https://doi.org/10.2210/pdb4RTW/pdb

• Classification: PROTEIN BINDING
• Organism(s): Gallus gallus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the c-Src-SH3 domain E93V/Q128R mutant 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.52 kDa 
• Atom Count: 1,336 
• Modeled Residue Count: 144 
• Deposited Residue Count: 161 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, C	61	Gallus gallus	Mutation(s): 2  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, D, E	13	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth C], I [auth D], J [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.94	α = 90
b = 36.94	β = 90
c = 83.42	γ = 120

Software Package:

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

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: 2024-10-30
  Changes: Structure summary