Research workbench
Sumo E1 activating enzyme SAE1-SAE2-mg-ATP complex
Analyse Sumo E1 activating enzyme SAE1-SAE2-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
- 1Y8Q
- Type
- protein
- Length
- 1,648 residues
- Chains
- 4
- 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
- Ligands
- ATP, MG, ZN
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like 1 activating enzyme E1A | protein | 313 | 45% helix, 20% strand | Q9UBE0 |
| B | Ubiquitin-like 2 activating enzyme E1B | protein | 510 | 39% helix, 16% strand | Q9UBT2 |
| C | Ubiquitin-like 1 activating enzyme E1A | protein | 311 | 41% helix, 19% strand | Q9UBE0 |
| D | Ubiquitin-like 2 activating enzyme E1B | protein | 514 | 38% helix, 16% strand | Q9UBT2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.74 | 0.80 | 75 | empty |
| 2 | 569 | 0.74 | 0.82 | 64 | MG, ATP |
| 3 | 390 | 0.74 | 0.85 | 43 | MG, ATP |
| 4 | 669 | 0.70 | 0.78 | 71 | empty |
| 5 | 768 | 0.66 | 0.74 | 72 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2569 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2510 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1Y8Q · Sumo E1 activating enzyme SAE1-SAE2-mg-ATP complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UBT2 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 2 (Q9UBT2) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q9UBE0 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 1 (Q9UBE0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 1Y8Q · PDBe 1Y8Q · UniProt Q9UBE0 · UniProt Q9UBT2
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