Research workbench
Crystal structure of the pmftn variant E130A soaked in iron (overnight)
Analyse Crystal structure of the pmftn variant E130A soaked in iron (overnight) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZLW
- Type
- protein
- Length
- 1,258 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 · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, C, F, H | Ferritin (EC 1.16.3.1) | protein | 157 | 80% helix, 1% strand | B6DMH6 |
| B | Ferritin (EC 1.16.3.1) | protein | 158 | 80% helix, 1% strand | B6DMH6 |
| E | Ferritin (EC 1.16.3.1) | protein | 158 | 80% helix, 1% strand | B6DMH6 |
| G | Ferritin (EC 1.16.3.1) | protein | 157 | 79% helix, 0% strand | B6DMH6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 37 copies · chains A, D, B, C, E, F, G, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.74 | 0.93 | 26 | empty |
| 2 | 174 | 0.71 | 0.89 | 25 | empty |
| 3 | 89 | 0.48 | 0.81 | 18 | empty |
| 4 | 122 | 0.44 | 0.77 | 21 | empty |
| 5 | 116 | 0.43 | 0.77 | 18 | empty |
Interfaces
14 interfaces between chains.
- A–E · 1028 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 1025 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 1022 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 516 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 506 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (alkylation).
Compared structures
- 4ZLW · Crystal structure of the PmFTN variant E130A 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 4ZLW · PDBe 4ZLW · UniProt B6DMH6
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