› 6plh

X-ray diffraction
1.6Å resolution

FAB fragment complexed with C-mannosylated tryptophan peptide

Released:
DOI: 10.2210/pdb6plh/pdb
PDB entry 6plh coloured by chain, front view.
PDB entry 6plh coloured by chain, side view.
PDB entry 6plh coloured by chain, top view.
Source organisms:
Primary publication:
Yeast- and antibody-based tools for studying tryptophan C-mannosylation.
John A, Järvå MA, Shah S, Mao R, Chappaz S, Birkinshaw RW, Czabotar PE, Lo AW, Scott NE, Goddard-Borger ED
Nat Chem Biol 17 428-437 (2021)
PMID: 33542533

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-232180 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fab 5G12 light chain Chain: A
Molecule details ›
Chain: A
Length: 219 amino acids
Theoretical weight: 24.12 KDa
Source organism: Mus musculus
Fab 5G12 heavy chain Chain: B
Molecule details ›
Chain: B
Length: 223 amino acids
Theoretical weight: 23.9 KDa
Source organism: Mus musculus
Interleukin-21 receptor Chain: C
Molecule details ›
Chain: C
Length: 37 amino acids
Theoretical weight: 4.3 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q9HBE5 (Residues: 202-232; Coverage: 6%)
Gene names: IL21R, NILR, UNQ3121/PRO10273

Ligands and Environments

2 bound ligands:
Ligand PO4 1 x PO4
Ligand MAN 1 x MAN
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P21
Unit cell:
a: 43.232Å b: 89.892Å c: 59.317Å
α: 90° β: 95.94° γ: 90°
R-values:
R R work R free
0.191 0.189 0.221
Expression system: Komagataella pastoris

Quick links

Citations

4 review citations

Protein C-Mannosylation and C-Mannosyl Tryptophan in Chemical Biology and Medicine.
Minakata et al. (2021)
3 more

1 mention without citation

Protein-Ligand CH-π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation.
Xiao et al. (2023)