4RTZ | pdb_00004rtz

Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide VSL12

• PDB DOI: https://doi.org/10.2210/pdb4RTZ/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: 0.98 Å
• R-Value Free: 
  0.158 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide VSL12

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: 8.37 kDa 
• Atom Count: 636 
• Modeled Residue Count: 69 
• Deposited Residue Count: 73 
• 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
VSL12 peptide	B	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.158 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.904	α = 90
b = 41.046	β = 90
c = 44.066	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoPROC	data scaling
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