1N47

Isolectin B4 from Vicia villosa in complex with the Tn antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 1N47

Classification: SUGAR BINDING PROTEIN

Total Structure Weight: 102737.59

Macromolecule Entities
Molecule Chains Length Organism Details
Isolectin B4 A, B, C, D 233 Vicia villosa Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TNR
Query on TNR

A, B, C, D O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)- L-SERINE
C11 H20 N2 O8
REDMNGDGDYFZRE-WKWISIMFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A, B, C, D ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B, C, D MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.188
  • Space Group: P 43

Unit Cell:

Length (Å) Angle (°)
a = 85.51 α = 90.00
b = 85.51 β = 90.00
c = 153.65 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-30
  • Released Date: 2003-02-25
  • Deposition author(s): Babino, A., Tello, D., Rojas, A., Bay, S., Osinaga, E., Alzari, P.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update