3SH3

Crystal structure of a pro-inflammatory lectin from the seeds of Dioclea wilsonii STANDL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Literature

Crystal structure of a pro-inflammatory lectin from the seeds of Dioclea wilsonii Standl.

Rangel, T.B.Rocha, B.A.Bezerra, G.A.Assreuy, A.M.Pires, A.F.Nascimento, A.S.Bezerra, M.J.Nascimento, K.S.Nagano, C.S.Sampaio, A.H.Gruber, K.Delatorre, P.Fernandes, P.M.Cavada, B.S.

(2012) Biochimie 94: 525-532

  • DOI: https://doi.org/10.1016/j.biochi.2011.09.001
  • Primary Citation of Related Structures:  
    3SH3

  • PubMed Abstract: 

    The crystal structure and pro-inflammatory property of a lectin from the seeds of Dioclea wilsonii (DwL) were analyzed to gain a better understanding of structure/function relationships of Diocleinae lectins. Following crystallization and structural determination by standard molecular replacement techniques, DwL was found to be a tetramer based on PISA analysis, and composed by two metal-binding sites per monomer and loops which are involved in molecular oligomerization. DwL presents 96% and 99% identity with two other previously described lectins of Dioclea rostrata (DRL) and Dioclea grandiflora (DGL). DwL differs structurally from DVL and DRL with regard to the conformation of the carbohydrate recognition domain and related biological activities. The structural analysis of DwL in comparison to other Diocleinae lectins can be related to the differences in the dose-dependent pro-inflammatory effect elicited in Wistar rats, probably via specific interactions with mast cells complex carbohydrate, resulting in significant paw edema. DwL appears to be involved in positive modulation of mast cell degranulation via recognition of surface carbohydrates. Since this recognition is dependent on site volume and CRD configuration, edematogenesis mediated by resident cells varies in potency and efficacy among different Diocleinae lectins.


  • Organizational Affiliation

    Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lectin alpha chain237Macropsychanthus wilsoniiMutation(s): 0 
UniProt
Find proteins for P86624 (Macropsychanthus wilsonii)
Explore P86624 
Go to UniProtKB:  P86624
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP86624
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XMM
Query on XMM

Download Ideal Coordinates CCD File 
D [auth A]5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside
C14 H15 Br Cl N O6
OPIFSICVWOWJMJ-HAAGFXOZSA-N
A3B
Query on A3B

Download Ideal Coordinates CCD File 
F [auth A]D-VINYLGLYCINE
C4 H7 N O2
RQVLGLPAZTUBKX-GSVOUGTGSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.82α = 90
b = 66.873β = 90
c = 107.345γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Structure summary