› 1ndd

X-ray diffraction
1.6Å resolution

STRUCTURE OF NEDD8

Released:
DOI: 10.2210/pdb1ndd/pdb
PDB entry 1ndd coloured by chain, front view.
PDB entry 1ndd coloured by chain, side view.
PDB entry 1ndd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes.
Whitby FG, Xia G, Pickart CM, Hill CP
J Biol Chem 273 34983-91 (1998)
PMID: 9857030

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172429 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NEDD8 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

2 bound ligands:
Ligand CL 2 x CL
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21
Unit cell:
a: 45.804Å b: 64.972Å c: 48.573Å
α: 90° β: 96.66° γ: 90°
R-values:
R R work R free
0.219 0.219 0.3
Expression system: Escherichia coli

Quick links

Citations

37 review citations

Mechanisms underlying ubiquitination.
Pickart CM. (2001)
36 more

21 mentions without citation

Substrate specificity of the ubiquitin and Ubl proteases.
Ronau et al. (2016)
20 more