6T9B

Crystal structrue of RSL W31A lectin mutant in complex with alpha-methylfucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification.

Houser, J.Kozmon, S.Mishra, D.Hammerova, Z.Wimmerova, M.Koca, J.

(2020) Chemistry 26: 10769-10780

  • DOI: https://doi.org/10.1002/chem.202000593
  • Primary Citation of Related Structures:  
    6T99, 6T9A, 6T9B

  • PubMed Abstract: 

    The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell-cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction, and non-polar dispersion interactions. The role of dispersion-driven CH-π interactions (stacking) in protein-carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. In this study, we analyzed the CH-π interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X-ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH-π stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol -1 . All the results show that the stacking CH-π interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.


  • 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-binding lectin protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I
90Ralstonia solanacearumMutation(s): 1 
Gene Names: RSP795_21825RSP799_05830RSP822_19650RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum)
Explore A0A0S4TLR1 
Go to UniProtKB:  A0A0S4TLR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4TLR1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MFU (Subject of Investigation/LOI)
Query on MFU

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
DA [auth H]
EA [auth H]
GA [auth I]
AA [auth G],
BA [auth G],
DA [auth H],
EA [auth H],
GA [auth I],
HA [auth I],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
V [auth E],
W [auth E],
Y [auth F],
Z [auth F]
methyl alpha-L-fucopyranoside
C7 H14 O5
OHWCAVRRXKJCRB-CXNFULCWSA-N
GLY
Query on GLY

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
IA [auth I]
L [auth A]
O [auth B]
CA [auth G],
FA [auth H],
IA [auth I],
L [auth A],
O [auth B],
R [auth C],
U [auth D],
X [auth E]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.914α = 90.04
b = 44.048β = 91
c = 103.461γ = 119.67
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2020-08-12
    Changes: Database references, Structure summary
  • Version 1.3: 2020-12-16
    Changes: Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description