1FAT

PHYTOHEMAGGLUTININ-L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystallographic structure of phytohemagglutinin-L.

Hamelryck, T.W.Dao-Thi, M.H.Poortmans, F.Chrispeels, M.J.Wyns, L.Loris, R.

(1996) J Biol Chem 271: 20479-20485

  • DOI: https://doi.org/10.1074/jbc.271.34.20479
  • Primary Citation of Related Structures:  
    1FAT

  • PubMed Abstract: 

    The structure of phytohemagglutinin-L (PHA-L), a leucoagglutinating seed lectin from Phaseolus vulgaris, has been solved with molecular replacement using the coordinates of lentil lectin as model, and refined at a resolution of 2.8 A. The final R-factor of the structure is 20.0%. The quaternary structure of the PHA-L tetramer differs from the structures of the concanavalin A and peanut lectin tetramers, but resembles the structure of the soybean agglutinin tetramer. PHA-L consists of two canonical legume lectin dimers that pack together through the formation of a close contact between two beta-strands. Of the two covalently bound oligosaccharides per monomer, only one GlcNAc residue per monomer is visible in the electron density. In this article we describe the structure of PHA-L, and we discuss the putative position of the high affinity adenine-binding site present in a number of legume lectins. A comparison with transthyretin, a protein that shows a remarkable resemblance to PHA-L, gives further ground to our proposal.


  • Organizational Affiliation

    Dienst Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 Sint-Genesius-Rode, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHYTOHEMAGGLUTININ-L
A, B, C, D
252Phaseolus vulgarisMutation(s): 0 
UniProt
Find proteins for P05087 (Phaseolus vulgaris)
Explore P05087 
Go to UniProtKB:  P05087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05087
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.3α = 90
b = 121.2β = 93.7
c = 90.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary