Research workbench
Crystal structure of a de novo designed hexameric helical-bundle protein
Analyse Crystal structure of a de novo designed hexameric helical-bundle protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TMS
- Type
- protein
- Length
- 835 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A novel designed pore protein; Affinity purification tag
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, D, H, I, J, K | A novel designed pore protein | protein | 69 | 88% helix, 0% strand | — |
| G, L | A novel designed pore protein | protein | 69 | 88% helix, 0% strand | — |
| Q | Affinity purification tag | protein | 3 | 0% helix, 0% strand | — |
| R | Affinity purification tag | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, E, F, D, H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.85 | 0.88 | 69 | SO4 |
| 2 | 774 | 0.84 | 0.86 | 70 | SO4 |
| 3 | 614 | 0.81 | 0.86 | 72 | empty |
| 4 | 205 | 0.65 | 0.84 | 26 | empty |
| 5 | 125 | 0.62 | 0.86 | 23 | empty |
Interfaces
21 interfaces between chains.
- C–E · 1390 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 1313 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 1259 Ų buried · 3 hydrogen bonds · protein-protein
- J–K · 1217 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1202 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6TMS · Crystal structure of a de novo designed hexameric helical-bundle protein · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6TMS · PDBe 6TMS
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.