› 6h78

X-ray diffraction
2.7Å resolution

E1 enzyme for ubiquitin like protein activation.

Released:
DOI: 10.2210/pdb6h78/pdb
PDB entry 6h78 coloured by chain, front view.
PDB entry 6h78 coloured by chain, side view.
PDB entry 6h78 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation.
Soudah N, Padala P, Hassouna F, Kumar M, Mashahreh B, Lebedev AA, Isupov MN, Cohen-Kfir E, Wiener R
J Mol Biol 431 463-478 (2019)
PMID: 30412706

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190465 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin-like modifier-activating enzyme 5 Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Length: 300 amino acids
Theoretical weight: 33.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9GZZ9 (Residues: 36-335; Coverage: 74%)
Gene names: UBA5, UBE1DC1
Sequence domains: ThiF family

Ligands and Environments

5 bound ligands:
Ligand ATP 16 x ATP
Ligand MG 32 x MG
Ligand ZN 16 x ZN
Ligand EDO 42 x EDO
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Spacegroup: P21
Unit cell:
a: 143.86Å b: 151.933Å c: 153.543Å
α: 90° β: 93.07° γ: 90°
R-values:
R R work R free
0.19 0.19 0.242
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Decrypting UFMylation: How Proteins Are Modified with UFM1.
Banerjee et al. (2020)
3 more