Research workbench
Capsid structure of the propionibacterium acnes bacteriophage ATCC_CLEAR
Analyse Capsid structure of the propionibacterium acnes bacteriophage ATCC_CLEAR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JB5
- Type
- protein
- Length
- 2,076 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- A4K473
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 2 distinct chains · 17% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Major capsid protein | protein | 300 | 14% helix, 26% strand | A4K473 |
| G | Major capsid protein | protein | 276 | 20% helix, 25% strand | A4K473 |
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 | 825 | 0.72 | 0.77 | 115 | empty |
| 2 | 509 | 0.71 | 0.80 | 62 | empty |
| 3 | 496 | 0.67 | 0.78 | 63 | empty |
| 4 | 611 | 0.66 | 0.76 | 79 | empty |
| 5 | 343 | 0.63 | 0.78 | 67 | empty |
Interfaces
15 interfaces between chains.
- B–C · 2318 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 2295 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 2290 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2275 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2266 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3JB5 · Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear · 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 A4K473
- Elsewhere: RCSB PDB 3JB5 · PDBe 3JB5 · UniProt A4K473
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