MolNFT v1 · #62475 · protein
Structural basis of iron transport gating in helicobacter pylori ferritin
3EGM: “Structural basis of iron transport gating in helicobacter pylori ferritin”. X-ray diffraction, 1 ligand (FE), 10 pockets (best druggability 0.54). MolNFT v1 #62475 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EGM
- 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
- 10 · best druggability 0.54
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, D, C, E, F
- GOL · Glycerol · additive · 3 copies · chains A, F, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.54 | 0.76 | 33 | empty |
| 2 | 228 | 0.51 | 0.76 | 28 | empty |
| 3 | 150 | 0.49 | 0.78 | 25 | empty |
| 4 | 141 | 0.48 | 0.79 | 27 | empty |
| 5 | 84 | 0.41 | 0.79 | 15 | empty |
Interfaces
8 interfaces between chains.
- B–E · 1434 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1430 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1415 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 831 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 825 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3EGM · Structural basis of iron transport gating in 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 3EGM · PDBe 3EGM · UniProt Q9ZLI1
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