Research workbench
Structural basis for the iron uptake mechanism of helicobacter pylori ferritin
Analyse Structural basis for the iron uptake mechanism of helicobacter pylori ferritin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BVF
- Type
- protein
- Length
- 1,032 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- Q9ZLI1
- Ligands
- FE
- Pockets
- 11 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ferritin (EC 1.16.3.1) | protein | 172 | 76% helix, 1% strand | Q9ZLI1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 15 copies · chains A, B, C, D, E, F
- IPA · Isopropyl alcohol · additive · 12 copies · chains A, C, B, D, E, F
- GOL · Glycerol · additive · 3 copies · chains C, D, B, E, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.52 | 0.76 | 25 | empty |
| 2 | 138 | 0.50 | 0.79 | 25 | IPA |
| 3 | 196 | 0.48 | 0.75 | 26 | empty |
| 4 | 133 | 0.47 | 0.78 | 26 | IPA |
| 5 | 79 | 0.41 | 0.79 | 14 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1426 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1411 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 1409 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 822 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 820 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3BVF · Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin · the same entry in another collection · chain F against F, TM-score 1.00
- Q9ZLI1 · AlphaFold monomer V2.0 prediction for bacterial non-heme ferritin (Q9ZLI1) · a predicted model of the same protein · chain F against A, TM-score 0.96
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 Q9ZLI1
- Elsewhere: RCSB PDB 3BVF · PDBe 3BVF · UniProt Q9ZLI1
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