Research workbench
Crystal structure of the pmftn variant E44H soaked in iron (45 min)
Analyse Crystal structure of the pmftn variant E44H soaked in iron (45 min) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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