Research workbench
T5 bacteriophage major capsid protein - one PB8 hexon
Analyse T5 bacteriophage major capsid protein - one PB8 hexon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TJT
- Type
- protein
- Length
- 1,752 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- Q6QGD8
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 21% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Major capsid protein | protein | 292 | 21% helix, 23% strand | Q6QGD8 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.82 | 0.83 | 131 | empty |
| 2 | 831 | 0.76 | 0.80 | 91 | empty |
| 3 | 364 | 0.64 | 0.79 | 56 | empty |
| 4 | 302 | 0.58 | 0.77 | 34 | empty |
| 5 | 331 | 0.58 | 0.76 | 32 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2409 Ų buried · 98 hydrogen bonds · protein-protein
- C–D · 2371 Ų buried · 64 hydrogen bonds · protein-protein
- B–C · 2350 Ų buried · 99 hydrogen bonds · protein-protein
- A–B · 2350 Ų buried · 138 hydrogen bonds · protein-protein
- A–F · 2310 Ų buried · 92 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 5TJT · T5 bacteriophage major capsid protein - one PB8 hexon · 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
- Every structure of UniProt Q6QGD8
- Elsewhere: RCSB PDB 5TJT · PDBe 5TJT · UniProt Q6QGD8
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