Research workbench
Insights into the ubiquitin transfer cascade from the refined structure of the activating enzyme for NEDD8
Analyse Insights into the ubiquitin transfer cascade from the refined structure of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YOV
- Type
- protein
- Length
- 1,834 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid protein-binding protein 1; Ubiquitin-activating enzyme E1C
- UniProt
- Q13564, Q8TBC4
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amyloid protein-binding protein 1 | protein | 529 | 51% helix, 10% strand | Q13564 |
| B | Ubiquitin-activating enzyme E1C | protein | 397 | 37% helix, 14% strand | Q8TBC4 |
| C | Amyloid protein-binding protein 1 | protein | 526 | 51% helix, 9% strand | Q13564 |
| D | Ubiquitin-activating enzyme E1C | protein | 382 | 32% helix, 14% strand | Q8TBC4 |
Ligands and binding sites
- 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
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 | 72 | 0.74 | 0.97 | 18 | empty |
| 2 | 56 | 0.72 | 0.98 | 18 | empty |
| 3 | 50 | 0.71 | 0.99 | 14 | empty |
| 4 | 380 | 0.70 | 0.82 | 47 | empty |
| 5 | 719 | 0.70 | 0.77 | 77 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3652 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 3331 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 553 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1YOV · Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8TBC4 · AlphaFold monomer V2.0 prediction for NEDD8-activating enzyme E1 catalytic subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q13564 · AlphaFold monomer V2.0 prediction for NEDD8-activating enzyme E1 regulatory subunit… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q13564
- Every structure of UniProt Q8TBC4
- Elsewhere: RCSB PDB 1YOV · PDBe 1YOV · UniProt Q13564 · UniProt Q8TBC4
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