Research workbench
Bullfrog M ferritin with IRON(III) bound to the ferroxidase site
Analyse Bullfrog M ferritin with IRON(III) bound to the ferroxidase site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RBC
- Type
- protein
- Length
- 4,148 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin, middle subunit
- EC
- 1.16.3.1
- UniProt
- P07798
- Ligands
- FE
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, K, M, O, Q, R, S, U, V, W, X | Ferritin, middle subunit (EC 1.16.3.1) | protein | 173 | 73% helix, 1% strand | P07798 |
| I, J, L, N, P | Ferritin, middle subunit (EC 1.16.3.1) | protein | 172 | 73% helix, 1% strand | P07798 |
| T | Ferritin, middle subunit (EC 1.16.3.1) | protein | 174 | 72% helix, 1% strand | P07798 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 50 copies · chains A, B, C, D, E, F, G, H, X, I, J, K, L, M, T, N, O, P, Q, R, S, U, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.77 | 0.97 | 21 | empty |
| 2 | 99 | 0.75 | 0.96 | 20 | empty |
| 3 | 191 | 0.75 | 0.90 | 27 | empty |
| 4 | 178 | 0.73 | 0.90 | 30 | empty |
| 5 | 163 | 0.72 | 0.90 | 24 | empty |
Interfaces
72 interfaces between chains.
- M–S · 1596 Ų buried · 28 hydrogen bonds · protein-protein
- E–I · 1595 Ų buried · 24 hydrogen bonds · protein-protein
- P–T · 1586 Ų buried · 31 hydrogen bonds · protein-protein
- N–R · 1570 Ų buried · 28 hydrogen bonds · protein-protein
- A–G · 1558 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3RBC · Bullfrog M ferritin with iron(III) bound to the ferroxidase site · the same entry in another collection · chain K against K, 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 P07798
- Elsewhere: RCSB PDB 3RBC · PDBe 3RBC · UniProt P07798
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