› 2oni

X-ray diffraction
2.2Å resolution

Catalytic Domain of the Human NEDD4-like E3 Ligase

Released:
DOI: 10.2210/pdb2oni/pdb
PDB entry 2oni coloured by chain, front view.
PDB entry 2oni coloured by chain, side view.
PDB entry 2oni coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Walker JR, Avvakumov GV, Xue S, Butler-Cole C, Weigelt J, Sundstrom M, Arrowsmith CH, Edwards AM, Bochkarev A, Dhe-Paganon S, Structural Genomics Consortium (SGC)

Function and Biology Details

Reactions catalysed: 
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-S-ubiquitinyl-L-cysteine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer
homo hexamer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188677 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase NEDD4-like Chain: A
Molecule details ›
Chain: A
Length: 392 amino acids
Theoretical weight: 47.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96PU5 (Residues: 594-967; Coverage: 38%)
Gene names: KIAA0439, NEDD4L, NEDL3
Sequence domains: HECT-domain (ubiquitin-transferase)
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand NA 1 x NA
1 modified residue:
Ligand MSE 14 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P6322
Unit cell:
a: 103.058Å b: 103.058Å c: 182.214Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.206 0.259
Expression system: Escherichia coli BL21(DE3)

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