Crystal structure of ubiquitin activating enzyme 1 (UBA1) in complex with the ub E2 UBC4, ubiquitin, and ATP/MG

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).

Ligands and binding sites

• ATP · Adenosine-5'-triphosphate · ligand · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A
• SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
• EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
• PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1669 Ų buried · 39 hydrogen bonds · protein-protein
• A–C · 1578 Ų buried · 14 hydrogen bonds · protein-protein
• B–C · 86 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 4II2 · Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4… · the same entry in another collection · chain A against A, TM-score 1.00
• O94609 · AlphaFold monomer V2.0 prediction for ubiquitin-activating enzyme E1 1 (O94609) · a predicted model of the same protein · chain A against A, TM-score 0.98
• P46595 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 4 (P46595) · a predicted model of the same protein · chain C against A, TM-score 0.97
• P0CH07 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P0CH07) · a predicted model of the same protein · chain B against A, TM-score 0.86

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt O94609
• Every structure of UniProt P0CH07
• Every structure of UniProt P46595
• Elsewhere: RCSB PDB 4II2 · PDBe 4II2 · UniProt O94609 · UniProt P0CH07 · UniProt P46595