7PVT

Crystal structure of the v-Src SH3 domain Q128R mutant in complex with the synthetic peptide VSL12

• PDB DOI: https://doi.org/10.2210/pdb7PVT/pdb

• Classification: PROTEIN BINDING
• Organism(s): Rous sarcoma virus (strain Schmidt-Ruppin E), unidentified
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-10-05 Released: 2022-09-14 
• Deposition Author(s): Camara-Artigas, A., Salinas-Garcia, M.C.
• Funding Organization(s): Ministry of Economy and Competitiveness (MINECO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

Crystal structure of the v-Src SH3 domain Q128R mutant in complex with the synthetic peptide VSL12

Camara-Artigas, A., Salinas Garcia, M.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.56 kDa 
• Atom Count: 1,094 
• Modelled Residue Count: 131 
• Deposited Residue Count: 146 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase transforming protein Src	A, C	61	Rous sarcoma virus (strain Schmidt-Ruppin E)	Mutation(s): 1  Gene Names: V-SRC EC: 2.7.10.2
UniProt
Find proteins for P63185 (Rous sarcoma virus subgroup E (strain Schmidt-Ruppin)) Explore P63185  Go to UniProtKB:  P63185

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VSL12	B, D	12	unidentified	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	F [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.227	α = 90
b = 51.227	β = 90
c = 46.34	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Camara-Artigas, A., Salinas-Garcia, M.C.

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Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness (MINECO)	Spain	BIO2006-78020-R

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description