1LOA

THREE-DIMENSIONAL STRUCTURES OF COMPLEXES OF LATHYRUS OCHRUS ISOLECTIN I WITH GLUCOSE AND MANNOSE: FINE SPECIFICITY OF THE MONOSACCHARIDE-BINDING SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structures of complexes of Lathyrus ochrus isolectin I with glucose and mannose: fine specificity of the monosaccharide-binding site.

Bourne, Y.Roussel, A.Frey, M.Rouge, P.Fontecilla-Camps, J.C.Cambillau, C.

(1990) Proteins 8: 365-376

  • DOI: 10.1002/prot.340080410
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of the methyl-alpha-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-alpha-D-mannopyranoside-LOL I complex was refined ...

    The structure of the methyl-alpha-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-alpha-D-mannopyranoside-LOL I complex was refined by simulated annealing using the program X-PLOR. The final R-factor value is 0.182 [Fo greater than 1 sigma(Fo)]. The isostructural methyl-alpha-D-glucopyranoside-LOL I complex was refined by X-Ray coupled energy minimization using the methyl-alpha-D-mannopyranoside-LOL I structure as a starting model to an R factor of 0.179 (all data). In both crystal forms, each dimer binds two molecules of sugar in pockets found near the calcium ions. The two saccharide moieties, which are in the C1 chair conformation, establish the same hydrogen bond pattern with the lectin. However, the van der Waals contacts are different between the O2, C2, C6, and O6 atoms of the two molecules and the backbone atoms of residues 208-211. Mannose, due to its axial C2 conformation, encloses the backbone atoms of the protein in a clamplike way. Van der Waals energy calculations suggest that this better complementarity of the mannoside molecule with the lectin could explain its higher affinity for isolectin I.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Studies of Two Isolectins from the Seeds of Lathyrus Ochrus
      Bourne, Y., Rouge, P., Cambillau, C.
      (1988) J Mol Biol 202: 685

    Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallisation des Macromolécules Biologiques, Faculté de Médecine, Marseille, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LEGUME ISOLECTIN I (BETA CHAIN)B, D, F, H52Lathyrus ochrusMutation(s): 0 
Find proteins for P12306 (Lathyrus ochrus)
Explore P12306 
Go to UniProtKB:  P12306
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEGUME ISOLECTIN I (ALPHA CHAIN)A, C, E, G181Lathyrus ochrusMutation(s): 0 
Find proteins for P04122 (Lathyrus ochrus)
Explore P04122 
Go to UniProtKB:  P04122
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GYP
Query on GYP

Download CCD File 
A, C, E, G
methyl alpha-D-glucopyranoside
C7 H14 O6
HOVAGTYPODGVJG-ZFYZTMLRSA-N
 Ligand Interaction
MN
Query on MN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.3α = 90
b = 139.8β = 91
c = 62.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    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