MolNFT v1 · #124723 · protein
Crystal structure of S. pombe ubiquitin E1 (UBA1) in complex with UBC15 and ubiquitin
5KNL · Ubiquitin-activating enzyme E1 1: “Crystal structure of S. pombe ubiquitin E1 (UBA1) in complex with UBC15 and ubiquitin”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.83). MolNFT v1 #124723 on GenesisL1: 3D…
- 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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