1OXC

LecB (PA-LII) in complex with FUCOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Carbohydrate Recognition by the Lectin LecB from Pseudomonas aeruginosa

Loris, R.Tielker, D.Jaeger, K.-E.Wyns, L.

(2003) J.MOL.BIOL. 331: 861-870

  • Primary Citation of Related Structures:  1OUR, 1OUS, 1OUX, 1OVP, 1OVS

  • PubMed Abstract: 
  • The crystal structure of Pseudomonas aeruginosa fucose-specific lectin LecB was determined in its metal-bound and metal-free state as well as in complex with fucose, mannose and fructopyranose. All three monosaccharides bind isosterically via direct ...

    The crystal structure of Pseudomonas aeruginosa fucose-specific lectin LecB was determined in its metal-bound and metal-free state as well as in complex with fucose, mannose and fructopyranose. All three monosaccharides bind isosterically via direct interactions with two calcium ions as well as direct hydrogen bonds with several side-chains. The higher affinity for fucose is explained by the details of the binding site around C6 and O1 of fucose. In the mannose and fructose complexes, a carboxylate oxygen atom and one or two hydroxyl groups are partly shielded from solvent upon sugar binding, preventing them from completely fulfilling their hydrogen bonding potential. In the fucose complex, no such defects are observed. Instead, C6 makes favourable interactions with a small hydrophobic patch. Upon demetallization, the C terminus as well as the otherwise rigid metal-binding loop become more mobile and adopt multiple conformations.


    Organizational Affiliation

    Vrije Universiteit Brussel, Laboratorium voor Ultrastructuur Instituut voor Moleculaire Biologie, Gebouw E, Pleinlaan 2, B-1050 Brussel, Belgium. reloris@vub.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical protein LecB
A, B, C, D
114Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)Gene Names: lecB
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  Q9HYN5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
A, D
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.088α = 90.00
b = 73.058β = 90.00
c = 99.889γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance