1N3P | pdb_00001n3p

Pterocarpus angolensis lectin in complex with sucrose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.217 (Depositor) 
  • R-Value Work: 
    0.178 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1N3P

This is version 2.1 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 Biological Chem 278: 16297-16303

  • DOI: https://doi.org/10.1074/jbc.M211148200
  • Primary Citation Related Structures: 
    1N3O, 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 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

Macromolecule Content 

  • Total Structure Weight: 56.03 kDa 
  • Atom Count: 3,962 
  • Modeled Residue Count: 482 
  • Deposited Residue Count: 504 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
lectin PAL
A, B
252Pterocarpus angolensisMutation(s): 0 
UniProt
Find proteins for Q8GSD2 (Pterocarpus angolensis)
Explore Q8GSD2 
Go to UniProtKB:  Q8GSD2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GSD2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G05551OP
GlyCosmos: G05551OP

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.217 (Depositor) 
  • R-Value Work:  0.178 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.83α = 90
b = 83.55β = 90
c = 123.39γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-13
    Changes: Data collection, Database references, Structure summary