3NV2

Crystal structure of human galectin-9 C-terminal CRD in complex with N-acetyllactosamine

Structural Biology Knowledgebase: 3NV2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 3NV2

Classification: Sugar Binding Protein

Total Structure Weight: 16172.16

Macromolecule Entities
Molecule Chains Length Organism Details
Galectin 9 short isoform variant A 138 Homo sapiens Fragment: C-terminal carbohydrate recognition domain, residues 186-323
Gene Name(s): LGALS9 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.179
  • Space Group: P 63
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.81 α = 90.00
b = 70.81 β = 90.00
c = 50.21 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-07-07
  • Released Date: 2010-09-22
  • Deposition author(s): Yoshida, H., Kamitori, S.

Revision History

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