5MB4

Crystal Structure of the Psathyrella asperospora lectin PAL in complex with GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Biophysical characterization and structural determination of the potent cytotoxic Psathyrella asperospora lectin.

Ribeiro, J.P.Ali Abol Hassan, M.Rouf, R.Tiralongo, E.May, T.W.Day, C.J.Imberty, A.Tiralongo, J.Varrot, A.

(2017) Proteins 85: 969-975

  • DOI: https://doi.org/10.1002/prot.25265
  • Primary Citation of Related Structures:  
    5MB4

  • PubMed Abstract: 

    A lectin with strong cytotoxic effect on human colon cancer HT29 and monkey kidney VERO cells was recently identified from the Australian indigenous mushroom Psathyrella asperospora and named PAL. We herein present its biochemical and structural analysis using a multidisciplinary approach. Glycan arrays revealed binding preference towards N-acetylglucosamine (GlcNAc) and, to a lesser extent, towards sialic acid (Neu5Ac). Submicromolar and millimolar affinity was measured by surface plasmon resonance for GlcNAc and NeuAc, respectively. The structure of PAL was resolved by X-ray crystallography, elucidating both the protein's amino acid sequence as well as the molecular basis rationalizing its binding specificity. Proteins 2017; 85:969-975. © 2016 Wiley Periodicals, Inc.


  • Organizational Affiliation

    CERMAV, UPR5301, CNRS and Université Grenoble Alpes, Grenoble, 38041, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GlcNAc specific lectin401PsathyrellaMutation(s): 0 
UniProt
Find proteins for A0A1U7Q1Z0 (Psathyrella)
Explore A0A1U7Q1Z0 
Go to UniProtKB:  A0A1U7Q1Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U7Q1Z0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
I [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NDG
Query on NDG

Download Ideal Coordinates CCD File 
J [auth A],
P [auth A]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
H [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.55α = 90
b = 120.55β = 90
c = 198.95γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Labex ArcaneFranceANR-11-LABX-0003-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary