› 1z3d

X-ray diffraction
2.5Å resolution

Protein crystal growth improvement leading to the 2.5A crystallographic structure of ubiquitin-conjugating enzyme (ubc-1) from Caenorhabditis elegans

Released:
DOI: 10.2210/pdb1z3d/pdb
PDB entry 1z3d coloured by chain, front view.
PDB entry 1z3d coloured by chain, side view.
PDB entry 1z3d coloured by chain, top view.
Source organism: Caenorhabditis elegans
Entry authors: Gavira JA, DiGiammarino E, Tempel W, Toh D, Liu ZJ, Wang BC, Meehan E, Ng JD, Southeast Collaboratory for Structural Genomics (SECSG)

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156554 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin-conjugating enzyme E2 1 Chain: A
Molecule details ›
Chain: A
Length: 157 amino acids
Theoretical weight: 17.95 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P52478 (Residues: 1-154; Coverage: 80%)
Gene names: C35B1.1, ubc-1
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P65
Unit cell:
a: 100.55Å b: 100.55Å c: 35.84Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.242 0.242 0.273
Expression system: Escherichia coli BL21

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