Research workbench
1.58 a structure of human apoferritin obtained from titan krios 2 at ebic, dls under commissioning session CM26464-2
Analyse 1.58 a structure of human apoferritin obtained from titan krios 2 at ebic, dls… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R5O
- Type
- protein
- Length
- 4,152 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy chain, N-terminally processed
- UniProt
- P02794
- Ligands
- NA
- Pockets
- 20 · best druggability 0.69
Structure
electron microscopy · 1 distinct chain · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Ferritin heavy chain, N-terminally processed | protein | 173 | 73% helix, 1% strand | P02794 |
Ligands and binding sites
- NA · Sodium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.69 | 0.84 | 38 | empty |
| 2 | 315 | 0.68 | 0.83 | 42 | empty |
| 3 | 298 | 0.68 | 0.83 | 40 | empty |
| 4 | 313 | 0.68 | 0.82 | 43 | empty |
| 5 | 300 | 0.67 | 0.83 | 41 | empty |
Interfaces
72 interfaces between chains.
- T–U · 1572 Ų buried · 32 hydrogen bonds · protein-protein
- Q–X · 1572 Ų buried · 32 hydrogen bonds · protein-protein
- D–K · 1571 Ų buried · 32 hydrogen bonds · protein-protein
- A–J · 1571 Ų buried · 32 hydrogen bonds · protein-protein
- E–N · 1566 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (oxidation).
Compared structures
- 7R5O · 1.58 A STRUCTURE OF HUMAN APOFERRITIN OBTAINED FROM TITAN KRIOS 2 AT eBIC, DLS UNDER… · 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 P02794
- Elsewhere: RCSB PDB 7R5O · PDBe 7R5O · UniProt P02794
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