4ODP

Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD.

Quistgaard, E.M.Weininger, U.Ural-Blimke, Y.Modig, K.Nordlund, P.Akke, M.Low, C.

(2016) BMC Biol 14: 82-82

  • DOI: https://doi.org/10.1186/s12915-016-0300-3
  • Primary Citation of Related Structures:  
    4ODK, 4ODL, 4ODM, 4ODN, 4ODO, 4ODP, 4ODQ, 4ODR

  • PubMed Abstract: 

    Peptidyl-prolyl isomerases (PPIases) catalyze cis/trans isomerization of peptidyl-prolyl bonds, which is often rate-limiting for protein folding. SlyD is a two-domain enzyme containing both a PPIase FK506-binding protein (FKBP) domain and an insert-in-flap (IF) chaperone domain. To date, the interactions of these domains with unfolded proteins have remained rather obscure, with structural information on binding to the FKBP domain being limited to complexes involving various inhibitor compounds or a chemically modified tetrapeptide.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera110Thermus thermophilusHomo sapiensMutation(s): 0 
Gene Names: TTHA0346FKBP1FKBP12FKBP1A
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SLE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLE7 
Go to UniProtKB:  Q5SLE7
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
GTEx:  ENSG00000088832 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ5SLE7P62942
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S216Escherichia coli K-12Mutation(s): 2 
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Explore P0A7V0 
Go to UniProtKB:  P0A7V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.69α = 90
b = 93.69β = 90
c = 93.69γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.2: 2017-10-04
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations