Macromolecules
Sequence Display for 1NXD

Classification: METAL BINDING PROTEIN

Total Structure Weight: 105996.42

Macromolecule Entities
Molecule Chains Length Organism Details
concanavalin A 1, 2, 3, 4 237 Canavalia ensiformis Mutation: E151D, R155E
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

1, 2, 3, 4 GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

1, 2, 3, 4 MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AZI
Query on AZI

1, 2, 3, 4 AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

1, 2, 3, 4 SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.184
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.30 α = 90.00
b = 118.00 β = 90.00
c = 249.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-10
  • Released Date: 2004-03-30
  • Deposition author(s): Lopez-Jaramillo, F.J., Gonzalez-Ramirez, L.A., Albert, A., Santoyo-Gonzalez, F., Vargas-Berenguel, A., Otalora, F.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4