Research workbench
Crystal structure of apo-ferritin from pseudo-nitzschia multiseries
Analyse Crystal structure of apo-ferritin from pseudo-nitzschia multiseries in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E6R
- Type
- protein
- Length
- 951 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- B6DMH6
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Ferritin (EC 1.16.3.1) | protein | 159 | 80% helix, 1% strand | B6DMH6 |
| B, C, E | Ferritin (EC 1.16.3.1) | protein | 158 | 79% helix, 0% strand | B6DMH6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.73 | 0.99 | 13 | empty |
| 2 | 180 | 0.71 | 0.88 | 28 | empty |
| 3 | 165 | 0.70 | 0.89 | 24 | empty |
| 4 | 167 | 0.57 | 0.81 | 18 | empty |
| 5 | 126 | 0.44 | 0.77 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–C · 982 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 502 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 501 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 473 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 470 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3E6R · Crystal structure of apo-ferritin from Pseudo-nitzschia multiseries · the same entry in another collection · chain A against A, 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 B6DMH6
- Elsewhere: RCSB PDB 3E6R · PDBe 3E6R · UniProt B6DMH6
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