Research workbench
Cryoem structure of pyocin R2 - precontracted - trunk
Analyse Cryoem structure of pyocin R2 - precontracted - trunk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PYT
- Type
- protein
- Length
- 6,624 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyocin tube PA0623; Pyocin sheath PA0622
- UniProt
- Q9I5S9, G3XD39
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| m, a, n, o, p, q, r, b, c, d, e, f | Pyocin tube PA0623 | protein | 167 | 7% helix, 49% strand | Q9I5S9 |
| M, A, N, O, P, Q, R, B, C, D, E, F | Pyocin sheath PA0622 | protein | 385 | 31% helix, 22% strand | G3XD39 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.79 | 0.81 | 99 | empty |
| 2 | 1031 | 0.78 | 0.80 | 85 | empty |
| 3 | 1034 | 0.78 | 0.80 | 98 | empty |
| 4 | 952 | 0.78 | 0.80 | 76 | empty |
| 5 | 975 | 0.78 | 0.80 | 72 | empty |
Interfaces
90 interfaces between chains.
- P–D · 2279 Ų buried · 30 hydrogen bonds · protein-protein
- R–F · 2274 Ų buried · 27 hydrogen bonds · protein-protein
- M–A · 2271 Ų buried · 25 hydrogen bonds · protein-protein
- Q–E · 2268 Ų buried · 26 hydrogen bonds · protein-protein
- O–C · 2265 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6PYT · CryoEM Structure of Pyocin R2 - precontracted - trunk · the same entry in another collection · chain m against m, 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
- Every structure of UniProt Q9I5S9
- Every structure of UniProt G3XD39
- Elsewhere: RCSB PDB 6PYT · PDBe 6PYT · UniProt Q9I5S9 · UniProt G3XD39
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.