MolNFT v1 · #55351 · protein
The idol-UBE2D complex mediates sterol-dependent degradation of the LDL receptor
2YHO · E3 ubiquitin-protein ligase mylip: “The idol-UBE2D complex mediates sterol-dependent degradation of the LDL receptor”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.60). MolNFT v1 #55351 on GenesisL1: 3D…
- PDB
- 2YHO
- Type
- protein
- Length
- 868 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase mylip; Ubiquitin-conjugating enzyme E2 D1
- EC
- 6.3.2.-, 6.3.2.19
- UniProt
- Q8WY64, P51668
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase mylip (EC 6.3.2.-) | protein | 67 | 22% helix, 22% strand | Q8WY64 |
| B, D, F | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 149 | 36% helix, 18% strand | P51668 |
| E, G | E3 ubiquitin-protein ligase mylip (EC 6.3.2.-) | protein | 70 | 20% helix, 21% strand | Q8WY64 |
| H | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 147 | 36% helix, 18% strand | P51668 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, C, F, D, E, G
- ACT · Acetate ion · additive · 9 copies · chains A, C, B, F, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.60 | 0.77 | 40 | empty |
| 2 | 365 | 0.60 | 0.76 | 32 | ACT |
| 3 | 306 | 0.59 | 0.77 | 37 | empty |
| 4 | 294 | 0.54 | 0.75 | 31 | ACT |
| 5 | 194 | 0.54 | 0.79 | 33 | empty |
Interfaces
10 interfaces between chains.
- E–G · 943 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 927 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 604 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 541 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 479 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2YHO · The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor · the same entry in another collection · chain H against H, TM-score 1.00
- P51668 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D1 (P51668) · a predicted model of the same protein · chain H against A, TM-score 0.98
- Q8WY64 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase mylip (Q8WY64) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q8WY64
- Every structure of UniProt P51668
- Elsewhere: RCSB PDB 2YHO · PDBe 2YHO · UniProt Q8WY64 · UniProt P51668
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