› 2zhm

X-ray diffraction
1.84Å resolution

Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine trimer (crystal 1)

Released:
DOI: 10.2210/pdb2zhm/pdb
PDB entry 2zhm coloured by chain, front view.
PDB entry 2zhm coloured by chain, side view.
PDB entry 2zhm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain.
Nagae M, Nishi N, Murata T, Usui T, Nakamura T, Wakatsuki S, Kato R
Glycobiology 19 112-7 (2009)
PMID: 18977853

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126137 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Galectin-9 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 148 amino acids
Theoretical weight: 16.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O00182 (Residues: 1-148; Coverage: 42%)
Gene name: LGALS9
Sequence domains: Galactoside-binding lectin
Structure domains: Jelly Rolls

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, GAL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, GAL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, GAL
Carbohydrate polymer
1 bound ligand:
Ligand RPN 2 x RPN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 35.217Å b: 67.964Å c: 219.964Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.182 0.235
Expression system: Escherichia coli

Quick links

Citations

7 review citations

TIM genes: a family of cell surface phosphatidylserine receptors that regulate innate and adaptive immunity.
Freeman et al. (2010)
6 more

5 mentions without citation

The Structural Biology of Galectin-Ligand Recognition: Current Advances in Modeling Tools, Protein Engineering, and Inhibitor Design.
Modenutti et al. (2019)
4 more