MolNFT v1 · #59351 · protein
Structural basis for the iron uptake mechanism of helicobacter pylori ferritin
3BVE: “Structural basis for the iron uptake mechanism of helicobacter pylori ferritin”. X-ray diffraction, 10 pockets (best druggability 0.51). MolNFT v1 #59351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BVE
- Type
- protein
- Length
- 1,037 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- Q9ZLI1
- Pockets
- 10 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ferritin (EC 1.16.3.1) | protein | 173 | 76% helix, 1% strand | Q9ZLI1 |
| E | Ferritin (EC 1.16.3.1) | protein | 172 | 76% helix, 1% strand | Q9ZLI1 |
| F | Ferritin (EC 1.16.3.1) | protein | 173 | 76% helix, 1% strand | Q9ZLI1 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains B, E, C, D, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.51 | 0.76 | 30 | empty |
| 2 | 199 | 0.49 | 0.76 | 27 | empty |
| 3 | 139 | 0.48 | 0.78 | 26 | empty |
| 4 | 109 | 0.48 | 0.80 | 20 | empty |
| 5 | 74 | 0.41 | 0.80 | 14 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1456 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1444 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1406 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 818 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 812 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3BVE · 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 3BVE · PDBe 3BVE · UniProt Q9ZLI1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.