2YY1

Crystal sturcture of N-terminal domain of human galectin-9 containing L-acetyllactosamine

Structural Biology Knowledgebase: 2YY1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 2YY1

Classification: SUGAR BINDING PROTEIN

Total Structure Weight: 17605.62

Macromolecule Entities
Molecule Chains Length Organism Details
Galectin-9 A 160 Homo sapiens Fragment: N-terminal domain, UNP residues 1-147
Gene Name(s): LGALS9 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NLC
Query on NLC

A 2-(ACETYLAMINO)-2-DEOXY-4-O-BETA-D-GALACTOPYRANOSYL- ALPHA-D-GLUCOPYRANOSE
C14 H25 N O11
KFEUJDWYNGMDBV-RCBHQUQDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NLC Kd: 490000 nM (97) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.211
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.41 α = 90.00
b = 47.41 β = 90.00
c = 121.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-04-27
  • Released Date: 2008-04-29
  • Deposition author(s): Kishishita, S., Nishino, A., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4