› 5tut

X-ray diffraction
2.6Å resolution

UbcH5a-Ub isopeptide conjugate

Released:
DOI: 10.2210/pdb5tut/pdb
PDB entry 5tut coloured by chain, front view.
PDB entry 5tut coloured by chain, side view.
PDB entry 5tut coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Sanchez JG, Wagner JM, Pornillos O

Function and Biology Details

Reactions 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
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143251 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 D1 Chain: A
Molecule details ›
Chain: A
Length: 150 amino acids
Theoretical weight: 16.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P51668 (Residues: 1-147; Coverage: 100%)
Gene names: SFT, UBC5A, UBCH5, UBCH5A, UBE2D1
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21
Unit cell:
a: 41.949Å b: 51.41Å c: 53.157Å
α: 90° β: 101.39° γ: 90°
R-values:
R R work R free
0.205 0.2 0.243
Expression system: Escherichia coli BL21(DE3)

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