4D52

CRYSTAL STRUCTURE OF FUCOSE BINDING LECTIN FROM ASPERGILLUS FUMIGATUS (AFL) IN COMPLEX WITH L-GALACTOPYRANOSE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Insights Into Aspergillus Fumigatus Lectin Specificity: Afl Binding Sites are Functionally Non-Equivalent.

Houser, J.Komarek, J.Cioci, G.Varrot, A.Imberty, A.Wimmerova, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 442

  • DOI: https://doi.org/10.1107/S1399004714026595
  • Primary Citation of Related Structures:  
    4AGT, 4AH4, 4AHA, 4C1Y, 4D4U, 4D52, 4UOU

  • PubMed Abstract: 

    The Aspergillus fumigatus lectin AFL was recently described as a new member of the AAL lectin family. As a lectin from an opportunistic pathogen, it might play an important role in the interaction of the pathogen with the human host. A detailed study of structures of AFL complexed with several monosaccharides and oligosaccharides, including blood-group epitopes, was combined with affinity data from SPR and discussed in the context of previous findings. Its six binding sites are non-equivalent, and owing to minor differences in amino-acid composition they exhibit a marked difference in specific ligand recognition. AFL displays a high affinity in the micromolar range towards oligosaccharides which were detected in plants and also those bound on the human epithelia. All of these results indicate AFL to be a complex member of the lectin family and a challenging target for future medical research and, owing to its binding properties, a potentially useful tool in specific biotechnological applications.


  • Organizational Affiliation

    Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FUCOSE-SPECIFIC LECTIN FLEA315Aspergillus fumigatusMutation(s): 0 
UniProt
Find proteins for Q4WW81 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q4WW81 
Go to UniProtKB:  Q4WW81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4WW81
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FUCOSE-SPECIFIC LECTIN FLEA
B, D
315Aspergillus fumigatusMutation(s): 0 
UniProt
Find proteins for Q4WW81 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q4WW81 
Go to UniProtKB:  Q4WW81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4WW81
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FUCOSE-SPECIFIC LECTIN FLEA315Aspergillus fumigatusMutation(s): 0 
UniProt
Find proteins for Q4WW81 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q4WW81 
Go to UniProtKB:  Q4WW81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4WW81
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
FA [auth C],
GA [auth C],
J [auth A],
RA [auth D],
U [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GIV
Query on GIV

Download Ideal Coordinates CCD File 
F [auth A]
KA [auth C]
LA [auth C]
M [auth A]
MA [auth C]
F [auth A],
KA [auth C],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
OA [auth D],
VA [auth D],
WA [auth D],
X [auth B],
Y [auth B],
Z [auth B]
beta-L-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-KGJVWPDLSA-N
GXL
Query on GXL

Download Ideal Coordinates CCD File 
BA [auth C]
DA [auth C]
E [auth A]
EA [auth C]
H [auth A]
BA [auth C],
DA [auth C],
E [auth A],
EA [auth C],
H [auth A],
I [auth A],
JA [auth C],
L [auth A],
PA [auth D],
Q [auth B],
QA [auth D],
S [auth B],
T [auth B],
UA [auth D]
alpha-L-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-SXUWKVJYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
HA [auth C],
SA [auth D],
V [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CA [auth C]
G [auth A]
IA [auth C]
K [auth A]
R [auth B]
CA [auth C],
G [auth A],
IA [auth C],
K [auth A],
R [auth B],
TA [auth D],
W [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
O [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

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AA [auth C],
NA [auth D],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
B, D
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.03α = 90
b = 70.44β = 108.34
c = 117.8γ = 90
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: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary