1NM7

Solution structure of the ScPex13p SH3 domain

• PDB DOI: https://doi.org/10.2210/pdb1NM7/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-01-09 Released: 2003-03-04 
• Deposition Author(s): Pires, J.R., Hong, X., Brockmann, C., Volkmer-Engert, R., Schneider-Mergener, J., Oschkinat, H., Erdmann, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

The ScPex13p SH3 Domain Exposes Two Distinct Binding Sites for Pex5p and Pex14p

Pires, J.R., Hong, X., Brockmann, C., Volkmer-Engert, R., Schneider-Mergener, J., Oschkinat, H., Erdmann, R.

(2003) J Mol Biol 326: 1427-1435

• PubMed: 12595255 
• DOI: https://doi.org/10.1016/s0022-2836(03)00039-1
• Primary Citation of Related Structures:  
  1NM7


• PubMed Abstract: 
  

  Pex13p is an essential component of the peroxisomal protein import machinery and interacts via its C-terminal SH3 domain with the type II SH3-ligand Pex14p and the non-PXXP protein Pex5p. We report the solution structure of the SH3 domain of Pex13p from Saccharomyces cerevisiae and the identification of a novel-binding pocket, which binds a non-PXXP-peptide representing the binding site of Pex5p. Chemical shift assays revealed the binding sites for Pex5p and Pex14p ligand peptides to be distinct and spatially separated. Competition assays demonstrated that the two ligand peptides can bind simultaneously to the SH3 domain.

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Organizational Affiliation: 

Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.09 kDa 
• Atom Count: 502 
• Modelled Residue Count: 61 
• Deposited Residue Count: 69 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal Membrane Protein PAS20	A	69	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P80667 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P80667  Go to UniProtKB:  P80667

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-04 
Deposition Author(s): Pires, J.R., Hong, X., Brockmann, C., Volkmer-Engert, R., Schneider-Mergener, J., Oschkinat, H., Erdmann, R.

Revision History  

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations