MolNFT v1 · #112411 · protein
Crystal structure of the pmftn variant E44Q soaked in iron (overnight)
4ZKH · Ferritin: “Crystal structure of the pmftn variant E44Q soaked in iron (overnight)”. X-ray diffraction, 1 ligand (FE), 13 pockets (best druggability 0.74). MolNFT v1 #112411 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4ZKH
- Type
- protein
- Length
- 1,266 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- B6DMH6
- Ligands
- FE
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ferritin (EC 1.16.3.1) | protein | 158 | 80% helix, 1% strand | B6DMH6 |
| D, B, F, H | Ferritin (EC 1.16.3.1) | protein | 159 | 79% helix, 0% strand | B6DMH6 |
| C, G | Ferritin (EC 1.16.3.1) | protein | 157 | 80% helix, 1% strand | B6DMH6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 31 copies · chains A, D, G, B, C, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.74 | 0.93 | 31 | empty |
| 2 | 55 | 0.73 | 0.99 | 10 | empty |
| 3 | 52 | 0.70 | 0.98 | 11 | empty |
| 4 | 178 | 0.70 | 0.88 | 24 | empty |
| 5 | 101 | 0.44 | 0.78 | 14 | empty |
Interfaces
14 interfaces between chains.
- A–E · 1065 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 1040 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 1012 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 505 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (alkylation).
Compared structures
- 4ZKH · Crystal structure of the PmFTN variant E44Q soaked in iron (overnight) · 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 4ZKH · PDBe 4ZKH · UniProt B6DMH6
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