Research workbench
Crystal structure of S. pombe ubiquitin E1 (UBA1) in complex with UBC15 and ubiquitin
Analyse Crystal structure of S. pombe ubiquitin E1 (UBA1) in complex with UBC15 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KNL
- Type
- protein
- Length
- 2,443 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1; Ubiquitin; Ubiquitin-conjugating enzyme E2 15
- EC
- 6.2.1.45, 2.3.2.23
- UniProt
- O94609, A0A081CFF0, Q9Y818
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 981 | 41% helix, 18% strand | O94609 |
| B, E | Ubiquitin | protein | 76 | 20% helix, 34% strand | A0A081CFF0 |
| C | Ubiquitin-conjugating enzyme E2 15 (EC 2.3.2.23) | protein | 171 | 33% helix, 18% strand | Q9Y818 |
| D | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 977 | 40% helix, 18% strand | O94609 |
| F | Ubiquitin-conjugating enzyme E2 15 (EC 2.3.2.23) | protein | 162 | 35% helix, 19% strand | Q9Y818 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.83 | 0.84 | 132 | empty |
| 2 | 1067 | 0.80 | 0.81 | 118 | empty |
| 3 | 700 | 0.76 | 0.81 | 83 | empty |
| 4 | 214 | 0.75 | 0.90 | 30 | empty |
| 5 | 562 | 0.74 | 0.82 | 65 | empty |
Interfaces
7 interfaces between chains.
- A–C · 2428 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 2096 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1683 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1669 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 936 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5KNL · Crystal structure of S. pombe ubiquitin E1 (Uba1) in complex with Ubc15 and ubiquitin · the same entry in another collection · chain F against F, 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 D against A, TM-score 0.97
- Q9Y818 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 15 (Q9Y818) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 A0A081CFF0
- Every structure of UniProt Q9Y818
- Elsewhere: RCSB PDB 5KNL · PDBe 5KNL · UniProt O94609 · UniProt A0A081CFF0 · UniProt Q9Y818
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