Research workbench
Crystal structures of ferritin mutants reveal side-on binding to diiron and end-on cleavage of oxygen
Analyse Crystal structures of ferritin mutants reveal side-on binding to diiron and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C6F
- Type
- protein
- Length
- 2,064 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial non-heme ferritin
- EC
- 1.16.3.2
- UniProt
- Q9ZLI1
- Ligands
- FE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Bacterial non-heme ferritin (EC 1.16.3.2) | protein | 172 | 77% helix, 1% strand | Q9ZLI1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 9 copies · chains A, B, D, F, G, I, K, J
- IMD · Imidazole · additive · 11 copies · chains A, B, C, D, E, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.82 | 0.83 | 98 | empty |
| 2 | 572 | 0.75 | 0.82 | 53 | empty |
| 3 | 302 | 0.57 | 0.77 | 40 | IMD |
| 4 | 277 | 0.54 | 0.75 | 29 | empty |
| 5 | 228 | 0.50 | 0.75 | 27 | empty |
Interfaces
19 interfaces between chains.
- I–J · 1488 Ų buried · 15 hydrogen bonds · protein-protein
- G–L · 1454 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1453 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1449 Ų buried · 13 hydrogen bonds · protein-protein
- H–K · 1445 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5C6F · Crystal structures of ferritin mutants reveal side-on binding to diiron and end-on… · the same entry in another collection · chain L against L, 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 Q9ZLI1
- Elsewhere: RCSB PDB 5C6F · PDBe 5C6F · UniProt Q9ZLI1
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