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Anaerobic crystal structure of iron soaked (75 min) ferritin from pseudo-nitzschia multiseries
Analyse Anaerobic crystal structure of iron soaked (75 min) ferritin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITW
- Type
- protein
- Length
- 1,254 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- UniProt
- B6DMH6
- Ligands
- FE
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Ferritin | protein | 156 | 79% helix, 1% strand | B6DMH6 |
| D, B, H | Ferritin | protein | 158 | 80% helix, 0% strand | B6DMH6 |
| C | Ferritin | protein | 156 | 79% helix, 1% strand | B6DMH6 |
| E | Ferritin | protein | 157 | 80% helix, 1% strand | B6DMH6 |
| G | Ferritin | protein | 155 | 79% helix, 0% strand | B6DMH6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, D, B, C, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.72 | 0.99 | 13 | empty |
| 2 | 200 | 0.70 | 0.87 | 23 | empty |
| 3 | 111 | 0.57 | 0.84 | 21 | empty |
| 4 | 125 | 0.55 | 0.82 | 13 | empty |
| 5 | 153 | 0.52 | 0.79 | 17 | empty |
Interfaces
15 interfaces between chains.
- A–E · 1091 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 1048 Ų buried · 5 hydrogen bonds · protein-protein
- C–H · 1043 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 487 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 476 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (alkylation).
Compared structures
- 4ITW · Anaerobic crystal structure of iron soaked (75 min) ferritin from Pseudo-nitzschia… · 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 4ITW · PDBe 4ITW · UniProt B6DMH6
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