PDBe 1xt9

X-ray diffraction
2.2Å resolution

Crystal Structure of Den1 in complex with Nedd8

Released:
Source organism: Homo sapiens

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Sentrin-specific protease 8 Chain: A
Molecule details ›
Chain: A
Length: 212 amino acids
Theoretical weight: 24.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW Q96LD8 (Residues: 1-212; Coverage: 100%)
Gene names: DEN1, FKSG8, NEDP1, PRSC2, SENP8
Sequence domains: Ulp1 protease family, C-terminal catalytic domain
Structure domains: Adenoviral Proteinase; Chain A
NEDD8 Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW 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

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P21212
Unit cell:
a: 68.849Å b: 71.626Å c: 52.947Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.209 0.259
Expression system: Escherichia coli