Research workbench
Sumo E1 activating enzyme SAE1-SAE2-SUMO1-mg-ATP complex
Analyse Sumo E1 activating enzyme SAE1-SAE2-SUMO1-mg-ATP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y8R
- Type
- protein
- Length
- 1,819 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like 1 activating enzyme E1A; Ubiquitin-like 2 activating enzyme E1B…
- UniProt
- Q9UBE0, Q9UBT2, P63165
- Ligands
- ATP, MG, ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like 1 activating enzyme E1A | protein | 314 | 42% helix, 20% strand | Q9UBE0 |
| B | Ubiquitin-like 2 activating enzyme E1B | protein | 512 | 37% helix, 16% strand | Q9UBT2 |
| C, F | Ubiquitin-like protein SMT3C | protein | 84 | 21% helix, 32% strand | P63165 |
| D | Ubiquitin-like 1 activating enzyme E1A | protein | 311 | 45% helix, 19% strand | Q9UBE0 |
| E | Ubiquitin-like 2 activating enzyme E1B | protein | 514 | 37% helix, 17% strand | Q9UBT2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains B, E
- ZN · Zinc ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.76 | 0.79 | 113 | MG, ATP |
| 2 | 915 | 0.74 | 0.78 | 100 | MG, ATP |
| 3 | 454 | 0.74 | 0.84 | 64 | empty |
| 4 | 70 | 0.74 | 0.98 | 16 | empty |
| 5 | 218 | 0.71 | 0.87 | 38 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2534 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2500 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1155 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1099 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 178 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1Y8R · Sumo E1 activating enzyme SAE1-SAE2-SUMO1-mg-ATP complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UBE0 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 1 (Q9UBE0) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q9UBT2 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 2 (Q9UBT2) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P63165 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 1 (P63165) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q9UBE0
- Every structure of UniProt Q9UBT2
- Every structure of UniProt P63165
- Elsewhere: RCSB PDB 1Y8R · PDBe 1Y8R · UniProt Q9UBE0 · UniProt Q9UBT2 · UniProt P63165
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