6XX3

Crystal structure of the c-Src SH3 domain H122R-Q128E mutant in complex with Cu(II) at pH 6.5 co-crystallized with methyl beta-cyclodextrin

• PDB DOI: https://doi.org/10.2210/pdb6XX3/pdb

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


• Deposited: 2020-01-26 Released: 2020-04-22 
• Deposition Author(s): Camara-Artigas, A.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 8.24 kDa 
• Atom Count: 562 
• Modelled Residue Count: 54 
• Deposited Residue Count: 61 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cyclic 2,3-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-2,6-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-3-O-methyl-alpha-D-glucopyranose	B	7		N/A
Glycosylation Resources
GlyTouCan:  G04274SM GlyCosmos:  G04274SM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU (Subject of Investigation/LOI)	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900086	B	methyl-beta-cyclodextrin	Oligosaccharide / Drug delivery

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.566	α = 90
b = 35.566	β = 90
c = 81.076	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: 2020-04-22 
Deposition Author(s): Camara-Artigas, A.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	BIO2016-78020-R

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2020-06-03
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary