Research workbench
S. pombe ubiquitin E1 complex with a ubiquitin-AMP mimic
Analyse S. pombe ubiquitin E1 complex with a ubiquitin-AMP mimic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O82
- Type
- protein
- Length
- 2,113 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.604
- Source
- Schizosaccharomyces pombe (strain 972 / ATCC 24843)
- Molecule
- Ubiquitin-activating enzyme E1 1; Ubiquitin-60S ribosomal protein L40
- EC
- 6.2.1.45
- UniProt
- O94609, P0CH07
- Ligands
- POP, JZU, MG, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.604 · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 986 | 42% helix, 18% strand | O94609 |
| B, D | Ubiquitin-60S ribosomal protein L40 | protein | 76 | 24% helix, 33% strand | P0CH07 |
| C | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 975 | 41% helix, 18% strand | O94609 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 3 copies · chains A, C
- JZU · 5'-deoxy-5'-(sulfamoylamino)adenosine · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, C
- EDO · 1,2-ethanediol · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.80 | 0.86 | 78 | empty |
| 2 | 1125 | 0.74 | 0.77 | 110 | empty |
| 3 | 477 | 0.73 | 0.83 | 53 | empty |
| 4 | 480 | 0.73 | 0.82 | 65 | empty |
| 5 | 60 | 0.71 | 0.97 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1575 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1565 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1109 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 277 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 94 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6O82 · S. pombe ubiquitin E1 complex with a ubiquitin-AMP mimic · 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 C against A, TM-score 0.99
- 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 0.91
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 6O82 · PDBe 6O82 · UniProt O94609 · UniProt P0CH07
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