8BQ3 | pdb_00008bq3

Crystal structure of human R13 mutant of the c-Src SH3 domain in complex with VSL12-peptide

• PDB DOI: https://doi.org/10.2210/pdb8BQ3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-11-18 Released: 2023-11-29 
• Deposition Author(s): Varejao, N., Navarro, S., Ventura, S., Reverter, D.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.281 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human R13 mutant of the c-Src SH3 domain in complex with VSL12-peptide

Varejao, N., Navarro, S., Ventura, S., Reverter, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.18 kDa 
• Atom Count: 509 
• Modeled Residue Count: 63 
• Deposited Residue Count: 98 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	86	Homo sapiens	Mutation(s): 0  Gene Names: SRC EC: 2.7.10.2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PRO-LEU-PRO	B	12	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.281 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.362	α = 90
b = 39.362	β = 90
c = 148.457	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Varejao, N., Navarro, S., Ventura, S., Reverter, D.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2021-124602OB-I00

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary