3UK9

Galactose-specific lectin from Dolichos lablab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Legume lectin
A, B, C, D, E
A, B, C, D, E, F, G, H
281Lablab purpureusMutation(s): 0 
UniProt
Find proteins for B3EWQ9 (Lablab purpureus)
Explore B3EWQ9 
Go to UniProtKB:  B3EWQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3EWQ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
M [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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DA [auth E]
K [auth A]
L [auth A]
MA [auth G]
Q [auth B]
DA [auth E],
K [auth A],
L [auth A],
MA [auth G],
Q [auth B],
V [auth C],
Z [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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CA [auth E]
GA [auth F]
HA [auth F]
I [auth A]
J [auth A]
CA [auth E],
GA [auth F],
HA [auth F],
I [auth A],
J [auth A],
KA [auth G],
LA [auth G],
P [auth B],
T [auth C],
U [auth C],
Y [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

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BA [auth D]
FA [auth E]
JA [auth F]
O [auth A]
OA [auth G]
BA [auth D],
FA [auth E],
JA [auth F],
O [auth A],
OA [auth G],
QA [auth H],
S [auth B],
X [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

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AA [auth D]
EA [auth E]
IA [auth F]
N [auth A]
NA [auth G]
AA [auth D],
EA [auth E],
IA [auth F],
N [auth A],
NA [auth G],
PA [auth H],
R [auth B],
W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.99α = 89.92
b = 84.13β = 76.01
c = 93.159γ = 77
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description