MolNFT v1 · #95518 · protein
Crystal structure of ferritin from pseudo-nitzschia multiseries soaked with zinc
4ISM: “Crystal structure of ferritin from pseudo-nitzschia multiseries soaked with zinc”. X-ray diffraction, 1 ligand (ZN), 18 pockets (best druggability 0.72). MolNFT v1 #95518 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ISM
- Type
- protein
- Length
- 1,263 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- UniProt
- B6DMH6
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferritin | protein | 157 | 79% helix, 1% strand | B6DMH6 |
| D, B, G | Ferritin | protein | 159 | 77% helix, 0% strand | B6DMH6 |
| C | Ferritin | protein | 155 | 80% helix, 1% strand | B6DMH6 |
| E, F, H | Ferritin | protein | 158 | 80% helix, 1% strand | B6DMH6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 32 copies · chains A, D, E, G, B, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.72 | 0.98 | 11 | empty |
| 2 | 50 | 0.72 | 0.99 | 10 | empty |
| 3 | 188 | 0.71 | 0.88 | 27 | empty |
| 4 | 88 | 0.56 | 0.85 | 20 | empty |
| 5 | 126 | 0.55 | 0.82 | 18 | empty |
Interfaces
15 interfaces between chains.
- A–E · 1087 Ų buried · 5 hydrogen bonds · protein-protein
- C–H · 1057 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 1053 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 524 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 523 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (alkylation).
Compared structures
- 4ISM · Crystal structure of ferritin from Pseudo-nitzschia multiseries soaked with zinc · 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 4ISM · PDBe 4ISM · UniProt B6DMH6
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