Research workbench
Crystal structure of iron soaked (overnight) ferritin from pseudo- nitzschia multiseries
Analyse Crystal structure of iron soaked (overnight) ferritin from pseudo- nitzschia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IWK
- Type
- protein
- Length
- 950 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- UniProt
- B6DMH6
- Ligands
- FE
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Ferritin | protein | 159 | 80% helix, 1% strand | B6DMH6 |
| B | Ferritin | protein | 157 | 80% helix, 0% strand | B6DMH6 |
| C, E | Ferritin | protein | 158 | 80% helix, 1% strand | B6DMH6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 24 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.71 | 0.87 | 27 | empty |
| 2 | 210 | 0.69 | 0.86 | 23 | empty |
| 3 | 155 | 0.56 | 0.81 | 19 | empty |
| 4 | 108 | 0.41 | 0.77 | 27 | empty |
| 5 | 76 | 0.40 | 0.79 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–C · 994 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 504 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 500 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 472 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 472 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 modified (alkylation).
Compared structures
- 4IWK · Crystal structure of iron soaked (overnight) ferritin from Pseudo-nitzschia multiseries · 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 B6DMH6
- Elsewhere: RCSB PDB 4IWK · PDBe 4IWK · UniProt B6DMH6
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