Research workbench
Apoferritin structure at 1.34 ångström resolution determined from a 300 kv titan krios G3I electron microscope with K3 detector
Analyse Apoferritin structure at 1.34 ångström resolution determined from a 300 kv… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K3V
- Type
- protein
- Length
- 4,128 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
- ZN, 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, 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 (EC 1.16.3.1) | protein | 172 | 73% helix, 1% strand | P02794 |
Ligands and binding sites
- ZN · Zinc ion · metal · 254 copies · chains A, M, S, E, I, F, T, B, P, V, L, R, C, G, U, K, O, D, J, X, Q, H, N, W
- NA · Sodium ion · metal · 80 copies · chains A, S, T, B, P, M, C, U, V, D, F, G, E, Q, X, H, J, K, I, R, W, L, N, O
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 | 102 | 0.80 | 0.99 | 18 | empty |
| 2 | 102 | 0.80 | 0.99 | 18 | empty |
| 3 | 102 | 0.80 | 0.99 | 18 | empty |
| 4 | 99 | 0.80 | 0.99 | 17 | empty |
| 5 | 102 | 0.80 | 0.99 | 18 | empty |
Interfaces
72 interfaces between chains.
- A–S · 1558 Ų buried · 29 hydrogen bonds · protein-protein
- K–W · 1558 Ų buried · 29 hydrogen bonds · protein-protein
- M–R · 1554 Ų buried · 29 hydrogen bonds · protein-protein
- O–V · 1554 Ų buried · 29 hydrogen bonds · protein-protein
- C–U · 1553 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7K3V · Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV Titan Krios… · the same entry in another collection · chain G against G, 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 7K3V · PDBe 7K3V · UniProt P02794
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