4ODR

Structure of SlyD delta-IF from Thermus thermophilus in complex with FK506


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.929 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.153 

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:  

  • 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-i ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera
A, B
110Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: FKBP1A (FKBP1, FKBP12)
EC: 5.2.1.8 5.2.1.8
Find proteins for Q5SLE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLE7
Find proteins for P62942 (Homo sapiens)
Go to Gene View: FKBP1A
Go to UniProtKB:  P62942
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

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Download CCD File 
A, B
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
K506
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.929 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.153 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.500α = 90.00
b = 72.500β = 90.00
c = 178.960γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2017-07-26
    Type: Refinement description, Source and taxonomy
  • Version 1.2: 2017-10-04
    Type: Database references