› 4znq

X-ray diffraction
1.9Å resolution

Crystal structure of Dln1 complexed with Man(alpha1-2)Man

Released:
DOI: 10.2210/pdb4znq/pdb
PDB entry 4znq coloured by chain, front view.
PDB entry 4znq coloured by chain, side view.
PDB entry 4znq coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein.
Jia N, Liu N, Cheng W, Jiang YL, Sun H, Chen LL, Peng J, Zhang Y, Ding YH, Zhang ZH, Wang X, Cai G, Wang J, Dong MQ, Zhang Z, Wu H, Wang HW, Chen Y, Zhou CZ
EMBO Rep 17 235-48 (2016)
PMID: 26711430

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176957 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Aerolysin-like protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 335 amino acids
Theoretical weight: 36.48 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5CZR5 (Residues: 1-315; Coverage: 100%)
Gene names: aep1, dln1, jac5, zgc:113413

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN
Carbohydrate polymer
6 bound ligands:
Ligand CL 2 x CL
Ligand PEG 3 x PEG
Ligand PGE 5 x PGE
Ligand PG4 1 x PG4
Ligand EPE 1 x EPE
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 57.169Å b: 95.553Å c: 147.707Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.219
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Molecular mechanism of pore formation by aerolysin-like proteins.
Podobnik et al. (2017)
7 more

2 mentions without citation

Functional Diversity of Novel Lectins with Unique Structural Features in Marine Animals.
Hatakeyama et al. (2023)
1 more