MolNFT v1 · #112430 · protein
Crystal structure of the pmftn variant E44H soaked in iron (45 min)
4ZL5 · Ferritin: “Crystal structure of the pmftn variant E44H soaked in iron (45 min)”. X-ray diffraction, 1 ligand (FE), 9 pockets (best druggability 0.53). MolNFT v1 #112430 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZL5
- Type
- protein
- Length
- 948 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
- FE
- Pockets
- 9 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, D, E | Ferritin (EC 1.16.3.1) | protein | 158 | 80% helix, 1% strand | B6DMH6 |
| C | Ferritin (EC 1.16.3.1) | protein | 157 | 80% helix, 1% strand | B6DMH6 |
| F | Ferritin (EC 1.16.3.1) | protein | 159 | 80% helix, 1% strand | B6DMH6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 24 copies · chains B, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.53 | 0.80 | 18 | empty |
| 2 | 95 | 0.50 | 0.82 | 17 | empty |
| 3 | 102 | 0.46 | 0.79 | 13 | empty |
| 4 | 101 | 0.45 | 0.79 | 14 | empty |
| 5 | 90 | 0.41 | 0.77 | 13 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1034 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 990 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 977 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 508 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 495 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (alkylation).
Compared structures
- 4ZL5 · Crystal structure of the PmFTN variant E44H soaked in iron (45 min) · the same entry in another collection · chain B against B, 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 4ZL5 · PDBe 4ZL5 · UniProt B6DMH6
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