6F5W

Photorhabdus asymbiotica lectin (PHL) in complex with propargyl-fucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Synthesis of alpha-l-Fucopyranoside-Presenting Glycoclusters and Investigation of Their Interaction with Photorhabdus asymbiotica Lectin (PHL).

Jancarikova, G.Herczeg, M.Fujdiarova, E.Houser, J.Kover, K.E.Borbas, A.Wimmerova, M.Csavas, M.

(2018) Chemistry 24: 4055-4068

  • DOI: https://doi.org/10.1002/chem.201705853
  • Primary Citation of Related Structures:  
    6F5W

  • PubMed Abstract: 

    Photorhabdus asymbiotica is a gram-negative bacterium that is not only as effective an insect pathogen as other members of the genus, but it also causes serious diseases in humans. The recently identified lectin PHL from P. asymbiotica verifiably modulates an immune response of humans and insects, which supports the idea that the lectin might play an important role in the host-pathogen interaction. Dimeric PHL contains up to seven l-fucose-specific binding sites per monomer, and in order to target multiple binding sites of PHL, α-l-fucoside-containing di-, tri- and tetravalent glycoclusters were synthesized. Methyl gallate and pentaerythritol were chosen as multivalent scaffolds, and the fucoclusters were built from the above-mentioned cores by coupling with different oligoethylene bridges and propargyl α-l-fucosides using 1,3-dipolar azide-alkyne cycloaddition. The interaction between fucoside derivates and PHL was investigated by several biophysical and biological methods, ITC and SPR measurements, hemagglutination inhibition assay, and an investigation of bacterial aggregation properties were carried out. Moreover, details of the interaction between PHL and propargyl α-l-fucoside as a monomer unit were revealed using X-ray crystallography. Besides this, the interaction with multivalent compounds was studied by NMR techniques. The newly synthesized multivalent fucoclusters proved to be up to several orders of magnitude better ligands than the natural ligand, l-fucose.


  • Organizational Affiliation

    Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lectin PHL
A, B
369Photorhabdus asymbioticaMutation(s): 0 
Gene Names: PAU_00698
UniProt
Find proteins for C7BLE4 (Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77))
Explore C7BLE4 
Go to UniProtKB:  C7BLE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7BLE4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KG1 (Subject of Investigation/LOI)
Query on KG1

Download Ideal Coordinates CCD File 
HA [auth B]
IA [auth B]
JA [auth B]
KA [auth B]
LA [auth B]
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
propadienyl 6-deoxy-alpha-L-galactopyranoside
C9 H14 O5
ZGNQHYGPHWSZCN-JTPBWFLFSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
FA [auth B],
GA [auth B],
L [auth A],
M [auth A],
N [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
U [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
V [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KG1 Binding MOAD:  6F5W Kd: 1.49e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.571α = 90
b = 80.571β = 90
c = 224.799γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary