4ODQ

Structure of SlyD delta-IF from Thermus thermophilus in complex with S3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1186/s12915-016-0300-3
  • Primary Citation of Related Structures:  
    4ODQ, 4ODR, 4ODK, 4ODL, 4ODM, 4ODN, 4ODO, 4ODP

  • 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 ...

    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

    Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22603, Hamburg, Germany. christian.loew@embl-hamburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimeraA110Thermus 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
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3B16Escherichia coli K-12Mutation(s): 1 
Gene Names: rpsCb3314JW3276
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Explore P0A7V3 
Go to UniProtKB:  P0A7V3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.56α = 90
b = 93.56β = 90
c = 93.56γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

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