Research workbench
Validated near-atomic resolution structure of bacteriophage EPSILON15 derived from cryo-EM and modeling
Analyse Validated near-atomic resolution structure of bacteriophage EPSILON15 derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J40
- Type
- protein
- Length
- 3,122 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP10; GP7
- UniProt
- Q858G5, Q858G8
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 13% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N, M, H, K, I, J, L | GP10 | protein | 111 | 0% helix, 5% strand | Q858G5 |
| A, F, B, G, D, C, E | GP7 | protein | 335 | 18% helix, 10% strand | Q858G8 |
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 | 684 | 0.86 | 0.90 | 94 | empty |
| 2 | 868 | 0.84 | 0.86 | 105 | empty |
| 3 | 685 | 0.83 | 0.88 | 71 | empty |
| 4 | 781 | 0.83 | 0.86 | 99 | empty |
| 5 | 690 | 0.82 | 0.87 | 102 | empty |
Interfaces
28 interfaces between chains.
- A–B · 2768 Ų buried · 28 hydrogen bonds · protein-protein
- D–C · 2759 Ų buried · 13 hydrogen bonds · protein-protein
- F–E · 2704 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 2655 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2621 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3J40 · Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from… · the same entry in another collection · chain N against N, 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 Q858G5
- Every structure of UniProt Q858G8
- Elsewhere: RCSB PDB 3J40 · PDBe 3J40 · UniProt Q858G5 · UniProt Q858G8
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