Research workbench
Crystal structure of S. pombe UBA1 in a closed conformation
Analyse Crystal structure of S. pombe UBA1 in a closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UM6
- Type
- protein
- Length
- 962 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1
- EC
- 6.2.1.45
- UniProt
- O94609
- Ligands
- 8EA, 8E7, SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 962 | 39% helix, 17% strand | O94609 |
Ligands and binding sites
- 8EA · N-(2-{[(4-chlorophenyl)methyl]disulfanyl}ethyl)decan-1-amine · ligand · chains A
- 8E7 · 2-(decylamino)ethane-1-thiol · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.83 | 0.86 | 91 | SO4 |
| 2 | 473 | 0.73 | 0.82 | 59 | 8EA |
| 3 | 114 | 0.59 | 0.85 | 16 | empty |
| 4 | 78 | 0.49 | 0.83 | 18 | empty |
| 5 | 159 | 0.48 | 0.77 | 28 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5UM6 · Crystal Structure of S. pombe Uba1 in a closed conformation · 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 0.76
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
- Elsewhere: RCSB PDB 5UM6 · PDBe 5UM6 · UniProt O94609
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