3UJO

Galactose-specific seed lectin from Dolichos lablab in complex with adenine and galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography.

Shetty, K.N.Latha, V.L.Rao, R.N.Nadimpalli, S.K.Suguna, K.

(2013) IUBMB Life 65: 633-644

  • DOI: 10.1002/iub.1177
  • Primary Citation of Related Structures:  
    3UJO, 3UJQ, 3UK9, 3UL2

  • PubMed Abstract: 
  • Crystal structure analysis of a galactose-specific lectin from a leguminous food crop Dolichos lablab (Indian lablab beans) has been carried out to obtain insights into its quaternary association and lectin-carbohydrate interactions. The analysis led to the identification of adenine binding sites at the dimeric interfaces of the heterotetrameric lectin ...

    Crystal structure analysis of a galactose-specific lectin from a leguminous food crop Dolichos lablab (Indian lablab beans) has been carried out to obtain insights into its quaternary association and lectin-carbohydrate interactions. The analysis led to the identification of adenine binding sites at the dimeric interfaces of the heterotetrameric lectin. Structural details of similar adenine binding were reported in only one legume lectin, Dolichos biflorus, before this study. Here, we present the structure of the galactose-binding D. lablab lectin at different pH values in the native form and in complex with galactose and adenine. This first structure report on this lectin also provides a high resolution atomic view of legume lectin-adenine interactions. The tetramer has two canonical and two DB58-like interfaces. The binding of adenine, a non-carbohydrate ligand, is found to occur at four hydrophobic sites at the core of the tetramer at the DB58-like dimeric interfaces and does not interfere with the carbohydrate-binding site. To support the crystallographic observations, the adenine binding was further quantified by carrying out isothermal calorimetric titration. By this method, we not only estimated the affinity of the lectin to adenine but also showed that adenine binds with negative cooperativity in solution.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Legume lectinA, B, C, D281Lablab purpureusMutation(s): 0 
UniProt
Find proteins for B3EWQ9 (Lablab purpureus)
Explore B3EWQ9 
Go to UniProtKB:  B3EWQ9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL (Subject of Investigation/LOI)
Query on GAL

Download Ideal Coordinates CCD File 
F [auth A], K [auth B], Q [auth C], W [auth D]beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
ADE
Query on ADE

Download Ideal Coordinates CCD File 
E [auth A], J [auth B], P [auth C], V [auth D]ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
O [auth B], U [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D], I [auth A], N [auth B], T [auth C], Z [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
G [auth A], L [auth B], R [auth C], X [auth D]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A], M [auth B], S [auth C], Y [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.78α = 90
b = 89.78β = 90
c = 123.89γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary