Research workbench
Structure of a 48-mer protein nanocage fabricated from its 24-mer analogue by subunit interface redesign
Analyse Structure of a 48-mer protein nanocage fabricated from its 24-mer analogue by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GN8
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy chain
- EC
- 1.16.3.1
- UniProt
- P02794
- Ligands
- CA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferritin heavy chain (EC 1.16.3.1) | protein | 162 | 73% helix, 1% strand | P02794 |
| B | Ferritin heavy chain (EC 1.16.3.1) | protein | 143 | 70% helix, 1% strand | P02794 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.74 | 0.98 | 15 | empty |
| 2 | 90 | 0.42 | 0.78 | 14 | empty |
| 3 | 78 | 0.41 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1521 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5GN8 · Structure of a 48-mer protein nanocage fabricated from its 24-mer analogue by subunit… · the same entry in another collection · chain A against A, TM-score 1.00
- P02794 · AlphaFold monomer V2.0 prediction for ferritin heavy chain (P02794) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P02794
- Elsewhere: RCSB PDB 5GN8 · PDBe 5GN8 · UniProt P02794
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