4ODO

Structure of SlyD from Thermus thermophilus in complex with FK506

• PDB DOI: https://doi.org/10.2210/pdb4ODO/pdb

• Classification: ISOMERASE, CHAPERONE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-10 Released: 2015-01-14 
• Deposition Author(s): Quistgaard, E.M., Low, C., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

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

• PubMed: 27664121 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.12 kDa 
• Atom Count: 4,385 
• Modelled Residue Count: 458 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase SlyD	A, B, C	158	Thermus thermophilus	Mutation(s): 0  Gene Names: TTHA0346 EC: 5.2.1.8
UniProt
Find proteins for Q5SLE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLE7  Go to UniProtKB:  Q5SLE7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FK5	H [auth A], K [auth B], O [auth C]	8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN C44 H69 N O12 QJJXYPPXXYFBGM-LFZNUXCKSA-N
BTB	J [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
GOL	N [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A], I [auth B], M [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], E [auth A], F [auth A], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.71	α = 85.74
b = 50.21	β = 68.92
c = 57.67	γ = 80.12

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Quistgaard, E.M., Low, C., Nordlund, P.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations