8BJD | pdb_00008bjd

Full length structure of LpMIP with bound inhibitor JK095


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.294 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.245 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Legionella pneumophila macrophage infectivity potentiator protein appendage domains modulate protein dynamics and inhibitor binding.

Wiedemann, C.Whittaker, J.J.Perez Carrillo, V.H.Goretzki, B.Dajka, M.Tebbe, F.Harder, J.M.Krajczy, P.R.Joseph, B.Hausch, F.Guskov, A.Hellmich, U.A.

(2023) Int J Biol Macromol 252: 126366-126366

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.126366
  • Primary Citation Related Structures: 
    8BJC, 8BJD, 8BJE, 8BK4, 8BK5, 8BK6

  • PubMed Abstract: 

    Macrophage infectivity potentiator (MIP) proteins are widespread in human pathogens including Legionella pneumophila, the causative agent of Legionnaires' disease and protozoans such as Trypanosoma cruzi. All MIP proteins contain a FKBP (FK506 binding protein)-like prolyl-cis/trans-isomerase domain that hence presents an attractive drug target. Some MIPs such as the Legionella pneumophila protein (LpMIP) have additional appendage domains of mostly unknown function. In full-length, homodimeric LpMIP, the N-terminal dimerization domain is linked to the FKBP-like domain via a long, free-standing stalk helix. Combining X-ray crystallography, NMR and EPR spectroscopy and SAXS, we elucidated the importance of the stalk helix for protein dynamics and inhibitor binding to the FKBP-like domain and bidirectional crosstalk between the different protein regions. The first comparison of a microbial MIP and a human FKBP in complex with the same synthetic inhibitor was made possible by high-resolution structures of LpMIP with a [4.3.1]-aza-bicyclic sulfonamide and provides a basis for designing pathogen-selective inhibitors. Through stereospecific methylation, the affinity of inhibitors to L. pneumophila and T. cruzi MIP was greatly improved. The resulting X-ray inhibitor-complex structures of LpMIP and TcMIP at 1.49 and 1.34 Å, respectively, provide a starting point for developing potent inhibitors against MIPs from multiple pathogenic microorganisms.


  • Organizational Affiliation
    • Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Jena, Germany.

Macromolecule Content 

  • Total Structure Weight: 23.31 kDa 
  • Atom Count: 1,639 
  • Modeled Residue Count: 208 
  • Deposited Residue Count: 208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase208Legionella pneumophilaMutation(s): 0 
Gene Names: C3927_03235
EC: 5.2.1.8
UniProt
Find proteins for Q5ZXE0 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZXE0 
Go to UniProtKB:  Q5ZXE0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZXE0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9QN

Query on 9QN



Download:Ideal Coordinates CCD File
B [auth A](1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-(hydroxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one
C21 H23 Cl2 N3 O4 S
SLQCBVGDPHQIBY-XMCHAPAWSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
C [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.294 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.245 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.752α = 90
b = 76.752β = 90
c = 103.597γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany390713860

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary