Research workbench
Crystal structures of a novel open pore ferritin from the hyperthermophilic archaeon archaeoglobus fulgidus
Analyse Crystal structures of a novel open pore ferritin from the hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S3Q
- Type
- protein
- Length
- 1,947 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- UniProt
- O29424
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, I, K, L | Ferritin | protein | 162 | 79% helix, 1% strand | O29424 |
| G | Ferritin | protein | 163 | 78% helix, 1% strand | O29424 |
| J | Ferritin | protein | 164 | 77% helix, 1% strand | O29424 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.62 | 0.77 | 56 | empty |
| 2 | 381 | 0.61 | 0.77 | 55 | empty |
| 3 | 390 | 0.61 | 0.77 | 66 | empty |
| 4 | 341 | 0.58 | 0.76 | 46 | empty |
| 5 | 347 | 0.55 | 0.75 | 52 | empty |
Interfaces
22 interfaces between chains.
- K–L · 1341 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 1338 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1337 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1329 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1323 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 97 modified (engineered).
Compared structures
- 1S3Q · Crystal structures of a novel open pore ferritin from the hyperthermophilic Archaeon… · 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 O29424
- Elsewhere: RCSB PDB 1S3Q · PDBe 1S3Q · UniProt O29424
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