PDBe 4xkl

X-ray diffraction
2.1Å resolution

Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin

Released:
Source organism: Homo sapiens

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin Chains: A, C
Molecule details ›
Chains: A, C
Length: 80 amino acids
Theoretical weight: 8.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62987 (Residues: 1-76; Coverage: 59%)
Gene names: UBA52, UBCEP2
Sequence domains: Ubiquitin family
Calcium-binding and coiled-coil domain-containing protein 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 33 amino acids
Theoretical weight: 3.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13137 (Residues: 414-446; Coverage: 7%)
Gene names: CALCOCO2, NDP52
Sequence domains: Autophagy receptor zinc finger-C2H2 domain

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 83.95Å b: 73.8Å c: 39.7Å
α: 90° β: 108.49° γ: 90°
R-values:
R R work R free
0.196 0.194 0.243
Expression system: Escherichia coli BL21(DE3)