Research workbench
Model of closed pentamer of the haliangium ochraceum encapsulin from symmetry expansion of icosahedral single particle reconstruction
Analyse Model of closed pentamer of the haliangium ochraceum encapsulin from symmetry… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OE2
- Type
- protein
- Length
- 1,375 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LINOCIN_M18 bacteriocin protein; Haliangium ochraceum encapsulated ferritin localisation…
- UniProt
- D0LZ74, D0LZ73
- Pockets
- 12 · best druggability 0.65
Structure
electron microscopy · 2 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | LINOCIN_M18 bacteriocin protein | protein | 266 | 37% helix, 30% strand | D0LZ74 |
| 1, 2, 3, 4, 5 | Haliangium ochraceum encapsulated ferritin localisation sequence | protein | 9 | 0% helix, 0% strand | D0LZ73 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.65 | 0.78 | 51 | empty |
| 2 | 433 | 0.64 | 0.78 | 50 | empty |
| 3 | 413 | 0.64 | 0.78 | 47 | empty |
| 4 | 399 | 0.64 | 0.78 | 48 | empty |
| 5 | 417 | 0.63 | 0.77 | 50 | empty |
Interfaces
10 interfaces between chains.
- A–B · 983 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 982 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 982 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 980 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 974 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7OE2 · Model of closed pentamer of the Haliangium ochraceum encapsulin from symmetry expansion… · 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 D0LZ74
- Every structure of UniProt D0LZ73
- Elsewhere: RCSB PDB 7OE2 · PDBe 7OE2 · UniProt D0LZ74 · UniProt D0LZ73
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