Research workbench
CryoEM structure of Klebsiella phage Kp9 tail complex applied with C6 symmetry
Analyse CryoEM structure of Klebsiella phage Kp9 tail complex applied with C6 symmetry in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y1C
- Type
- protein
- Length
- 2,650 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.13
- Source
- Klebsiella phage Kp9
- Molecule
- phage connector protein; phage tail tubular protein A; phage tail tubular protein B…
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.13 · 6 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | phage connector protein | protein | 506 | 51% helix, 12% strand | — |
| W, X | phage tail tubular protein A | protein | 192 | 45% helix, 11% strand | — |
| Y | phage tail tubular protein B | protein | 790 | 5% helix, 38% strand | — |
| e | phage type I tail fiber | protein | 153 | 22% helix, 26% strand | — |
| f | phage type I tail fiber | protein | 156 | 23% helix, 29% strand | — |
| g | phage type I tail fiber | protein | 155 | 23% helix, 25% strand | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.86 | 0.87 | 114 | empty |
| 2 | 1121 | 0.85 | 0.85 | 94 | empty |
| 3 | 742 | 0.80 | 0.84 | 70 | empty |
| 4 | 501 | 0.72 | 0.81 | 69 | empty |
| 5 | 205 | 0.69 | 0.87 | 35 | empty |
Interfaces
17 interfaces between chains.
- A–L · 5642 Ų buried · 68 hydrogen bonds · protein-protein
- e–f · 2131 Ų buried · 30 hydrogen bonds · protein-protein
- e–g · 2121 Ų buried · 30 hydrogen bonds · protein-protein
- f–g · 1746 Ų buried · 23 hydrogen bonds · protein-protein
- W–X · 1500 Ų buried · 13 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7Y1C · PDBe 7Y1C
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