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1.56 a structure of human apoferritin obtained from data subset of titan mono-bcor microscope
Analyse 1.56 a structure of human apoferritin obtained from data subset of titan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z9F
- Type
- protein
- Length
- 4,152 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy chain
- EC
- 1.16.3.1
- UniProt
- P02794
- Ligands
- NA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, 1, K, a, B, E, e, r, G, I, M, O, Q, S, U, W, Y, 2, 4, F, H, P, X, 6 | Ferritin heavy chain (EC 1.16.3.1) | protein | 173 | 73% helix, 1% strand | P02794 |
Ligands and binding sites
- NA · Sodium ion · metal · 32 copies · chains A, e, F, 1, E, Y, K, a, B, O, P, r, G, I, M, Q, S, U, W, 2, 4, H, X, 6
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 | 0.80 | 0.99 | 16 | empty |
| 2 | 100 | 0.79 | 0.99 | 16 | empty |
| 3 | 93 | 0.79 | 0.99 | 18 | empty |
| 4 | 100 | 0.79 | 0.99 | 16 | empty |
| 5 | 88 | 0.79 | 0.99 | 18 | empty |
Interfaces
72 interfaces between chains.
- B–S · 1587 Ų buried · 34 hydrogen bonds · protein-protein
- 1–F · 1587 Ų buried · 34 hydrogen bonds · protein-protein
- U–4 · 1586 Ų buried · 34 hydrogen bonds · protein-protein
- e–X · 1585 Ų buried · 34 hydrogen bonds · protein-protein
- r–Y · 1581 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (oxidation).
Compared structures
- 6Z9F · 1.56 A structure of human apoferritin obtained from data subset of Titan Mono-BCOR… · the same entry in another collection · chain I against I, 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 6Z9F · PDBe 6Z9F · UniProt P02794
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