1VAL

CONCANAVALIN A COMPLEX WITH 4'-NITROPHENYL-ALPHA-D-GLUCOPYRANOSIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of the complexes of concanavalin A with 4'-nitrophenyl-alpha-D-mannopyranoside and 4'-nitrophenyl-alpha-D-glucopyranoside.

Kanellopoulos, P.N.Pavlou, K.Perrakis, A.Agianian, B.Vorgias, C.E.Mavrommatis, C.Soufi, M.Tucker, P.A.Hamodrakas, S.J.

(1996) J Struct Biol 116: 345-355

  • DOI: 10.1006/jsbi.1996.0052
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Concanavalin A (Con A) is the best-known plant lectin and has important in vitro biological activities arising from its specific saccharide-binding ability. Its exact biological role still remains unknown. The complexes of Con A with 4'-nitrophenyl-a ...

    Concanavalin A (Con A) is the best-known plant lectin and has important in vitro biological activities arising from its specific saccharide-binding ability. Its exact biological role still remains unknown. The complexes of Con A with 4'-nitrophenyl-alpha-D-mannopyranoside (alpha-PNM) and 4'-nitrophenyl-alpha-D-glucopyranoside (alpha-PNG) have been crystallized in space group P2(1)2(1)2 with cell dimensions a = 135.19 A, b = 155.38 A, c = 71.25 A and a = 134.66 A, b = 155.67 A, and c = 71.42 A, respectively. X-ray diffraction intensities to 2.75 A for the alpha-PNM and to 3.0 A resolution for the alpha-PNG complex have been collected. The structures of the complexes were solved by molecular replacement and refined by simulated annealing methods to crystallographic R-factor values of 0.185/0.186 and free-R-factor values of 0.260/0.274, respectively. In both structures, the asymmetric unit contains four molecules arranged as a tetramer, with approximate 222 symmetry. A saccharide molecule is bound in the sugar-binding site near the surface of each monomer. The nonsugar (aglycon) portion of the compounds used helps to identify the exact orientation of the saccharide in the sugar-binding pocket and is involved in major interactions between tetramers. The hydrogen bonding network in the region of the binding site has been analyzed, and only minor differences with the previously reported Con A-methyl-alpha-D-mannopyranoside complex structure have been observed. Structural differences that may contribute to the slight preference of the lectin for mannosides over glucosides are discussed. Calculations indicate a negative electrostatic surface potential for the saccharide binding site of Con A, which may be important for its biological activity. It is also shown in detail how a particular class of hydrophobic ligands interact with one of the three so-called characteristic hydrophobic sites of the lectins.


    Organizational Affiliation

    Europeam Molecular Biology Laboratory, Heidelberg, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CONCANAVALIN AA, B, C, D237Canavalia ensiformisMutation(s): 0 
Find proteins for P02866 (Canavalia ensiformis)
Explore P02866 
Go to UniProtKB:  P02866
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNG
Query on PNG

Download CCD File 
A, B, C, D
4-nitrophenyl alpha-D-glucopyranoside
C12 H15 N O8
IFBHRQDFSNCLOZ-ZIQFBCGOSA-N
 Ligand Interaction
MN
Query on MN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.66α = 90
b = 155.67β = 90
c = 71.42γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary