Research workbench
Haddock calculated model of LIN5001 bound to the het-S amyloid
Analyse Haddock calculated model of LIN5001 bound to the het-S amyloid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2MUS
- Type
- protein
- Length
- 355 residues
- Chains
- 5
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heterokaryon incompatibility protein S
- UniProt
- Q03689
- Ligands
- 3LS
- Pockets
- 3 · best druggability 0.77
Structure
solution nmr · 1 distinct chain · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Heterokaryon incompatibility protein S | protein | 71 | 4% helix, 48% strand | Q03689 |
Ligands and binding sites
- 3LS · 3''',4'-bis(carboxymethyl)-2,2':5',2'':5'',2''':5''',2''''-quinquethiophene-5,5''''-dicarboxylic acid · ligand · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.77 | 0.87 | 74 | empty |
| 2 | 429 | 0.66 | 0.79 | 79 | empty |
| 3 | 100 | 0.44 | 0.79 | 22 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1906 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 1825 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 1678 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 1651 Ų buried · 41 hydrogen bonds · protein-protein
- C–E · 127 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2MUS · HADDOCK calculated model of LIN5001 bound to the HET-s amyloid · the same entry in another collection · chain A against A, TM-score 1.00
- Q03689 · AlphaFold monomer V2.0 prediction for heterokaryon incompatibility protein S (Q03689) · a predicted model of the same protein · chain A against A, TM-score 0.68
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 Q03689
- Elsewhere: RCSB PDB 2MUS · PDBe 2MUS · UniProt Q03689
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