Research workbench
Crystal structures of ferritin mutants reveal diferric-peroxo intermediates
Analyse Crystal structures of ferritin mutants reveal diferric-peroxo intermediates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZTT
- Type
- protein
- Length
- 977 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial non-heme ferritin
- EC
- 1.16.3.2
- UniProt
- C9QT34
- Ligands
- FEO, FE, FE2, OH, O, OXY, PER
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Bacterial non-heme ferritin (EC 1.16.3.2) | protein | 162 | 80% helix, 1% strand | C9QT34 |
| B, F | Bacterial non-heme ferritin (EC 1.16.3.2) | protein | 164 | 79% helix, 1% strand | C9QT34 |
| E | Bacterial non-heme ferritin (EC 1.16.3.2) | protein | 163 | 79% helix, 1% strand | C9QT34 |
Ligands and binding sites
- FEO · Mu-oxo-diiron · ligand · 3 copies · chains A, B, E
- FE · Fe (III) ion · metal · 5 copies · chains C, D, F
- FE2 · Fe (II) ion · metal · 2 copies · chains C, E
- OH · Hydroxide ion · ion · 9 copies · chains A, B, C, D, E, F
- O · Oxygen atom · ion · 2 copies · chains F
- OXY · Oxygen molecule · ion · chains C
- PER · Peroxide ion · ion · chains D
- GOL · Glycerol · additive · 14 copies · chains A, C, B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.65 | 0.78 | 48 | empty |
| 2 | 402 | 0.62 | 0.77 | 54 | GOL |
| 3 | 89 | 0.48 | 0.82 | 21 | GOL |
| 4 | 120 | 0.48 | 0.79 | 21 | GOL |
| 5 | 82 | 0.42 | 0.79 | 19 | GOL |
Interfaces
8 interfaces between chains.
- C–D · 1253 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1197 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 1175 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 455 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 452 Ų buried · 4 hydrogen bonds · protein-protein
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 C9QT34
- Elsewhere: RCSB PDB 4ZTT · PDBe 4ZTT · UniProt C9QT34
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