4U36

Crystal structure of a seed lectin from Vatairea macrocarpa complexed with Tn-antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

High-resolution structure of a new Tn antigen-binding lectin from Vatairea macrocarpa and a comparative analysis of Tn-binding legume lectins.

Sousa, B.L.Silva Filho, J.C.Kumar, P.Pereira, R.I.yskowski, A.Rocha, B.A.Delatorre, P.Bezerra, G.A.Nagano, C.S.Gruber, K.Cavada, B.S.

(2014) Int J Biochem Cell Biol 59C: 103-110

  • DOI: 10.1016/j.biocel.2014.12.002
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Plant lectins have been studied as histological markers and promising antineoplastic molecules for a long time, and structural characterization of different lectins bound to specific cancer epitopes has been carried out successfully. The crystal stru ...

    Plant lectins have been studied as histological markers and promising antineoplastic molecules for a long time, and structural characterization of different lectins bound to specific cancer epitopes has been carried out successfully. The crystal structures of Vatairea macrocarpa (VML) seed lectin in complex with GalNAc-α-O-Ser (Tn antigen) and GalNAc have been determined at the resolution of 1.4Å and 1.7Å, respectively. Molecular docking analysis of this new structure and other Tn-binding legume lectins to O-mucin fragments differently decorated with this antigen provides a comparative binding profile among these proteins, stressing that subtle alterations that may not influence monosaccharide binding can, nonetheless, directly impact the ability of these lectins to recognize naturally occurring antigens. In addition to the specific biological effects of VML, the structural and binding similarities between it and other lectins commonly used as histological markers (e.g., VVLB4 and SBA) strongly suggest VML as a candidate tool for cancer research.


    Organizational Affiliation

    Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Av. Mister Hull s/n, Bloco 907, Box 6043, 60440-970 Fortaleza, Ceará, Brazil. Electronic address: bscavada@ufc.br.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seed lectin
A
240Vatairea macrocarpaMutation(s): 0 
Find proteins for P81371 (Vatairea macrocarpa)
Go to UniProtKB:  P81371
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TNR
Query on TNR

Download CCD File 
A
O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE
C11 H20 N2 O8
REDMNGDGDYFZRE-WKWISIMFSA-N
 Ligand Interaction
CIT
Query on CIT

Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.076α = 90
b = 85.808β = 90
c = 129.057γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil--
CAPESBrazil--

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.3: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence