1NPL

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSEUDONARCISSUS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,3-MANNOSE

Structural Biology Knowledgebase: 1NPL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 1NPL

Classification: SUGAR BINDING PROTEIN

Total Structure Weight: 13863.74

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (AGGLUTININ) A 109 Narcissus pseudonarcissus Mutation: Y15F, S17N, Y18N, Q27E, N35D, V48L, S49D, S50R, G51R, T58S, R67P, K68R
Details: FROM DAFFODIL PLANT FAMILY OF AMARYLLIDACEAE
Gene Name(s): LECNPA 7
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MAN N/A in BindingDB
Kd: 2000000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.187
  • Space Group: C 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 73.30 α = 90.00
b = 101.20 β = 90.00
c = 37.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-12-17
  • Released Date: 1998-12-23
  • Deposition author(s): Sauerborn, M.K., Wright, L.M., Reynolds, C.D., Grossmann, J.G., Rizkallah, P.J.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4