1N5Z | pdb_00001n5z

Complex structure of Pex13p SH3 domain with a peptide of Pex14p

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.273 (Depositor) 
  • R-Value Work: 
    0.244 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1N5Z

This is version 1.3 of the entry. See complete history. 

Literature

Topography for Independent Binding of alpha-Helical and PPII-Helical Ligands to a Peroxisomal SH3 Domain

Douangamath, A., Filipp, F.V., Klein, A.T.J., Barnett, P., Zou, P., Voorn-Brouwer, T., Vega, M.C., Mayans, O.M., Sattler, M., Distel, B., Wilmanns, M.

(2002) Mol Cell 10: 1007-1017

  • DOI: https://doi.org/10.1016/s1097-2765(02)00749-9
  • Primary Citation Related Structures: 
    1JQQ, 1N5Z

  • PubMed Abstract: 

    While the function of most small signaling domains is confined to binary ligand interactions, the peroxisomal Pex13p SH3 domain has the unique capacity of binding to two different ligands, Pex5p and Pex14p. We have used this domain as a model to decipher its structurally independent ligand binding sites. By the combined use of X-ray crystallography, NMR spectroscopy, and circular dichroism, we show that the two ligands bind in unrelated conformations to patches located at opposite surfaces of this SH3 domain. Mutations in the Pex13p SH3 domain that abolish interactions within the Pex13p-Pex5p interface specifically impair PTS1-dependent protein import into yeast peroxisomes.

    • Organizational Affiliation: 
    • EMBL-Hamburg, c/o Deutsches Elektronen Synchrotron, Notkestrasse 85, D-22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 24.96 kDa 
  • Atom Count: 1,344 
  • Modeled Residue Count: 160 
  • Deposited Residue Count: 212 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisomal membrane protein PAS20A,
C [auth B]		92Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P80667 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P80667 
Go to UniProtKB:  P80667
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80667
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
14-mer peptide from Peroxisomal membrane protein PEX14B [auth P],
D [auth Q]		14N/AMutation(s): 0 
UniProt
Find proteins for P53112 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53112 
Go to UniProtKB:  P53112
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53112
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.273 (Depositor) 
  • R-Value Work:  0.244 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.35α = 90
b = 63.204β = 90
c = 66.935γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BEASTmodel building
REFMACrefinement
BEASTphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references