5OB0 | pdb_00005ob0

Crystal structure of the c-Src-SH3 domain Q128E mutant in complex with the high affinity peptide APP12

• PDB DOI: https://doi.org/10.2210/pdb5OB0/pdb

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


• Deposited: 2017-06-25 Released: 2017-07-12 
• Deposition Author(s): Camara-Artigas, A.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 
  0.149 (Depositor), 0.138 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the c-Src-SH3 domain Q128E 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 generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 8.42 kDa 
• Atom Count: 676 
• Modeled Residue Count: 70 
• 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): 1  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	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: 1.17 Å
• R-Value Free:  0.149 (Depositor), 0.138 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.63	α = 90
b = 32.56	β = 103.02
c = 65.262	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Camara-Artigas, A.

---

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-78020-R

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2018-01-24
  Changes: Source and taxonomy
• Version 1.3: 2019-02-20
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary