S. pombe ubiquitin E1~UBIQUITIN-AMP tetrahedral intermediate mimic

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).

Ligands and binding sites

• VMX · 5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine · ligand · 2 copies · chains A, B, C, D
• CA · Calcium ion · metal · 2 copies · chains A, C
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains A, B, C, D
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1647 Ų buried · 38 hydrogen bonds · protein-protein
• C–D · 1629 Ų buried · 37 hydrogen bonds · protein-protein
• A–D · 415 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 6O83 · S. pombe ubiquitin E1~ubiquitin-AMP tetrahedral intermediate mimic · the same entry in another collection · chain A against A, TM-score 1.00
• 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 0.92
• O94609 · AlphaFold monomer V2.0 prediction for ubiquitin-activating enzyme E1 1 (O94609) · a predicted model of the same protein · chain C against A, TM-score 0.78

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
• Elsewhere: RCSB PDB 6O83 · PDBe 6O83 · UniProt O94609 · UniProt P0CH07