1N3O

Pterocarcpus angolensis lectin in complex with alpha-methyl glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Pterocarpus angolensis lectin in complex with glucose, sucrose, and turanose

Loris, R.Imberty, A.Beeckmans, S.Van Driessche, E.Read, J.S.Bouckaert, J.De Greve, H.Buts, L.Wyns, L.

(2003) J.BIOL.CHEM. 278: 16297-16303

  • DOI: 10.1074/jbc.M211148200
  • Primary Citation of Related Structures:  1N3P, 1N3Q

  • PubMed Abstract: 
  • The crystal structure of the Man/Glc-specific seed lectin from Pterocarpus angolensis was determined in complex with methyl-alpha-d-glucose, sucrose, and turanose. The carbohydrate binding site contains a classic Man/Glc type specificity loop. Its me ...

    The crystal structure of the Man/Glc-specific seed lectin from Pterocarpus angolensis was determined in complex with methyl-alpha-d-glucose, sucrose, and turanose. The carbohydrate binding site contains a classic Man/Glc type specificity loop. Its metal binding loop on the other hand is of the long type, different from what is observed in other Man/Glc-specific legume lectins. Glucose binding in the primary binding site is reminiscent of the glucose complexes of concanavalin A and lentil lectin. Sucrose is found to be bound in a conformation similar as seen in the binding site of lentil lectin. A direct hydrogen bond between Ser-137(OG) to Fru(O2) in Pterocarpus angolensis lectin replaces a water-mediated interaction in the equivalent complex of lentil lectin. In the turanose complex, the binding site of the first molecule in the asymmetric unit contains the alphaGlc1-3betaFruf form of furanose while the second molecule contains the alphaGlc1-3betaFrup form in its binding site.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lectin PAL
A, B
252Pterocarpus angolensisN/A
Find proteins for Q8GSD2 (Pterocarpus angolensis)
Go to UniProtKB:  Q8GSD2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GYP
Query on GYP

Download SDF File 
Download CCD File 
A, B
METHYL-ALPHA-D-GLUCOPYRANOSIDE
ALPHA-METHYL-D-GLUCOPYRANOSIDE
C7 H14 O6
HOVAGTYPODGVJG-ZFYZTMLRSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.760α = 90.00
b = 83.550β = 90.00
c = 122.930γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance