Research workbench
Molecular mechanism for the binding between sharpin and hoip
Analyse Molecular mechanism for the binding between sharpin and hoip in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X0W
- Type
- protein
- Length
- 864 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31; Sharpin
- EC
- 6.3.2.-
- UniProt
- Q96EP0, Q9H0F6
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 129 | 69% helix, 0% strand | Q96EP0 |
| C | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 130 | 66% helix, 0% strand | Q96EP0 |
| E | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 143 | 73% helix, 0% strand | Q96EP0 |
| G | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 140 | 71% helix, 0% strand | Q96EP0 |
| B | Sharpin | protein | 82 | 22% helix, 34% strand | Q9H0F6 |
| D | Sharpin | protein | 84 | 19% helix, 32% strand | Q9H0F6 |
| F | Sharpin | protein | 86 | 21% helix, 33% strand | Q9H0F6 |
| H | Sharpin | protein | 70 | 11% helix, 27% strand | Q9H0F6 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.73 | 0.76 | 104 | empty |
| 2 | 507 | 0.71 | 0.81 | 56 | empty |
| 3 | 134 | 0.71 | 0.91 | 26 | empty |
| 4 | 132 | 0.47 | 0.78 | 27 | empty |
| 5 | 172 | 0.46 | 0.75 | 22 | empty |
Interfaces
10 interfaces between chains.
- E–F · 890 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 806 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 806 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 642 Ų buried · 1 hydrogen bond · protein-protein
- G–H · 614 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5X0W · Molecular mechanism for the binding between Sharpin and HOIP · the same entry in another collection · chain H against H, TM-score 1.00
- Q96EP0 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF31 (Q96EP0) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q9H0F6 · AlphaFold monomer V2.0 prediction for sharpin (Q9H0F6) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q96EP0
- Every structure of UniProt Q9H0F6
- Elsewhere: RCSB PDB 5X0W · PDBe 5X0W · UniProt Q96EP0 · UniProt Q9H0F6
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