4J9D | pdb_00004j9d

Crystal structure of the N114A mutant of the Abl-SH3 domain complexed with the high affinity peptide P0

• PDB DOI: https://doi.org/10.2210/pdb4J9D/pdb

• Classification: Transferase/unknown function
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-02-16 Released: 2014-01-29 
• Deposition Author(s): Camara-Artigas, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the N114A mutant of the Abl-SH3 domain complexed with the high affinity peptide P0

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.22 kDa 
• Atom Count: 1,805 
• Modeled Residue Count: 204 
• Deposited Residue Count: 222 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ABL1	A, C, E	63	Homo sapiens	Mutation(s): 1  Gene Names: ABL, ABL1, JTK7 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens) Explore P00519  Go to UniProtKB:  P00519
PHAROS:  P00519 GTEx:  ENSG00000097007

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P0	B, D, F	11	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3L3 (Homo sapiens) Explore Q9Y3L3  Go to UniProtKB:  Q9Y3L3
PHAROS:  Q9Y3L3 GTEx:  ENSG00000100092

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.38	α = 90
b = 86.38	β = 90
c = 44.95	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Camara-Artigas, A.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2014-10-15
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary