› 7f5q

X-ray diffraction
2.3Å resolution

The crystal structure of VyPAL2 peptide asparaginyl ligase in its active enzyme form

Released:
DOI: 10.2210/pdb7f5q/pdb
PDB entry 7f5q coloured by chain, front view.
PDB entry 7f5q coloured by chain, side view.
PDB entry 7f5q coloured by chain, top view.
Source organism: Viola philippica
Primary publication:
Structural basis for proenzyme maturation, substrate recognition, and ligation by a hyperactive peptide asparaginyl ligase.
Hu S, El Sahili A, Kishore S, Wong YH, Hemu X, Goh BC, Sang Z, Wang Z, Tam JP, Liu CF, Lescar J
Plant Cell (2022)
PMID: 36099055

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-105282 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Legumain prodomain domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 282 amino acids
Theoretical weight: 31.13 KDa
Source organism: Viola philippica
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: A0A509GV09 (Residues: 50-332; Coverage: 61%)
Sequence domains: Peptidase C13 family

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 3 x NAG
Ligand EDO 7 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P212121
Unit cell:
a: 63.57Å b: 63.88Å c: 151.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.175 0.217
Expression system: Spodoptera frugiperda

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Citations

1 review citation

The role of forkhead-associated (FHA)-domain proteins in plant biology.
Wang Q. (2023)
2 other articles