› 5nl5

X-ray diffraction
1.96Å resolution

Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb

Released:
DOI: 10.2210/pdb5nl5/pdb
PDB entry 5nl5 coloured by chain, front view.
PDB entry 5nl5 coloured by chain, side view.
PDB entry 5nl5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Aggregation Pathways of Native-Like Ubiquitin Promoted by Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium.
Fermani S, Calvaresi M, Mangini V, Falini G, Bottoni A, Natile G, Arnesano F
Chemistry 24 4140-4148 (2018)
PMID: 29266436

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143231 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 76 amino acids
Theoretical weight: 8.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

3 bound ligands:
Ligand ZN 5 x ZN
Ligand ACT 3 x ACT
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 44.32Å b: 50.46Å c: 93.87Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.171 0.237
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

The pros and cons of ubiquitination on the formation of protein condensates.
Hou et al. (2023)